| Amed to Gili Trawangan | 🇮🇩 🇮🇩 | | Freebird Express, Arjuna Fast Cruise | | ~Apr-Oct |
| Ao Nang to Koh Phi Phi | 🇹🇭 🇹🇭 | 1h 30m to 2h | Satun Pakbara Speed Boat Club | | ~Oct-May |
| Ao Thammachat to Koh Chang | 🇹🇭 🇹🇭 | 25m to 35m | Koh Chang Ferry | 84 | ~Nov-Apr |
| Bacolod to Cagayan de Oro | 🇵🇭 🇵🇭 | 20h | 2GO Travel | 1 | year round |
| Bacolod to Iloilo | 🇵🇭 🇵🇭 | 1h to 1h 30m | 3 operators | 77 | year round |
| Bajoe to Kolaka | 🇮🇩 🇮🇩 | | ASDP Indonesia Ferry, Jembatan Nusantara | | year round |
| Bakauheni to Merak | 🇮🇩 🇮🇩 | 1h to 2h | 3 operators | 168 | year round |
| Balikpapan to Makassar | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Balikpapan to Tarakan | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Batam to Tanjung Balai Karimun | 🇮🇩 🇮🇩 | 3h | Pelni | 2 | year round |
| Batangas to Abra de Ilog | 🇵🇭 🇵🇭 | 2h 30m | Montenegro Shipping Lines | 21 | year round |
| Batangas to Bacolod | 🇵🇭 🇵🇭 | 25h | 2GO Travel | 1 | year round |
| Batangas to Calapan | 🇵🇭 🇵🇭 | 1h 10m to 3h | 5 operators | 147 | year round |
| Batangas to Caticlan | 🇵🇭 🇵🇭 | 8h to 11h | 3 operators | 14 | year round |
| Batangas to Iloilo | 🇵🇭 🇵🇭 | 17h | 2GO Travel | 1 | year round |
| Batangas to Odiongan | 🇵🇭 🇵🇭 | 9h to 10h | 3 operators | 10 | year round |
| Batangas to Puerto Galera | 🇵🇭 🇵🇭 | 1h to 2h | Montenegro Shipping Lines | 28 | year round |
| Batangas to Roxas City (Capiz) | 🇵🇭 🇵🇭 | 15h 30m to 18h | 2GO Travel, Starlite Ferries | 5 | year round |
| Bato (Leyte) to Ubay (Bohol) | 🇵🇭 🇵🇭 | 3h 30m | Medallion Transport | 7 | year round |
| Batulicin to Makassar | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Baubau to Ambon | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Benoa (Bali) to Lembar (Lombok) | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Bima to Labuan Bajo | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Bima to Waingapu (Sumba) | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Brunei (Serasa) to Labuan | 🇲🇾 🇧🇳 | 2h to 2h 15m | Maritime and Port Authority of Brunei Darussalam | 10 | year round |
| Bulalacao to Caticlan | 🇵🇭 🇵🇭 | 3h 30m | FastCat | 7 | year round |
| Butterworth to George Town (Penang) | 🇲🇾 🇲🇾 | 20m to 25m | Penang Port | 238 | year round |
| Cagayan de Oro to Iloilo | 🇵🇭 🇵🇭 | 13h | 2GO Travel | 1 | year round |
| Cagayan de Oro to Jagna (Bohol) | 🇵🇭 🇵🇭 | 5h 30m to 6h | Cokaliong Shipping Lines, Lite Ferries | 14 | year round |
| Caticlan to Odiongan | 🇵🇭 🇵🇭 | 3h to 4h | 2GO Travel, Starlite Ferries | 5 | year round |
| Caticlan to Roxas (Oriental Mindoro) | 🇵🇭 🇵🇭 | 3h | Montenegro Shipping Lines, Starlite Ferries | 14 | year round |
| Caticlan to Roxas City (Capiz) | 🇵🇭 🇵🇭 | 5h | 2GO Travel | 2 | year round |
| Cebu to Cagayan de Oro | 🇵🇭 🇵🇭 | 8h to 12h 30m | 4 operators | 23 | year round |
| Cebu to Dapitan | 🇵🇭 🇵🇭 | 10h to 15h | Starlite Ferries, Cokaliong Shipping Lines | 6 | year round |
| Cebu to Davao | 🇵🇭 🇵🇭 | 20h 30m | 2GO Travel | 1 | year round |
| Cebu to Dipolog | 🇵🇭 🇵🇭 | 12h | Medallion Transport | 3 | year round |
| Cebu to Dumaguete | 🇵🇭 🇵🇭 | 4h 20m to 6h | OceanJet, Cokaliong Shipping Lines | 21 | year round |
| Cebu to General Santos | 🇵🇭 🇵🇭 | 47h 30m | 2GO Travel | 1 | year round |
| Cebu to Getafe (Bohol) | 🇵🇭 🇵🇭 | 1h 15m | OceanJet | 7 | year round |
| Cebu to Iligan | 🇵🇭 🇵🇭 | 14h 30m to 15h | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 6 | year round |
| Cebu to Iloilo | 🇵🇭 🇵🇭 | 12h to 14h 45m | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 8 | year round |
| Cebu to Larena (Siquijor) | 🇵🇭 🇵🇭 | 9h to 10h | Starlite Ferries, Lite Ferries | 6 | year round |
| Cebu to Lazi (Siquijor) | 🇵🇭 🇵🇭 | 10h | Trans-Asia Shipping Lines | 3 | year round |
| Cebu to Maasin (Southern Leyte) | 🇵🇭 🇵🇭 | 3h to 6h 30m | 3 operators | 18 | year round |
| Cebu to Masbate | 🇵🇭 🇵🇭 | 12h to 14h 45m | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 6 | year round |
| Cebu to Nasipit (Butuan) | 🇵🇭 🇵🇭 | 12h | Cokaliong Shipping Lines, Starlite Ferries | 7 | year round |
| Cebu to Ormoc | 🇵🇭 🇵🇭 | 3h to 7h | 4 operators | 35 | year round |
| Cebu to Ozamiz | 🇵🇭 🇵🇭 | 10h to 11h | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 8 | year round |
| Cebu to Palompon (Leyte) | 🇵🇭 🇵🇭 | 3h to 6h | OceanJet, Cokaliong Shipping Lines | 11 | year round |
| Cebu to Siquijor | 🇵🇭 🇵🇭 | 4h 20m | OceanJet | 7 | year round |
| Cebu to Surigao | 🇵🇭 🇵🇭 | 5h 30m to 10h | 3 operators | 14 | year round |
| Cebu to Tacloban | 🇵🇭 🇵🇭 | 5h to 9h 30m | Roble Shipping, Trans-Asia Shipping Lines | 10 | year round |
| Cebu to Tagbilaran | 🇵🇭 🇵🇭 | 2h to 4h | 6 operators | 64 | year round |
| Cebu to Tubigon | 🇵🇭 🇵🇭 | 1h to 2h | 3 operators | 35 | year round |
| Chumphon to Koh Tao | 🇹🇭 🇹🇭 | 1h 45m to 2h 45m | 3 operators | | ~Nov-Apr |
| Coron to El Nido | 🇵🇭 🇵🇭 | 3h 30m | Montenegro Shipping Lines, Jomalia Shipping | 14 | year round |
| Coron to Puerto Princesa | 🇵🇭 🇵🇭 | 13h | 2GO Travel | 1 | year round |
| Davao to Bitung (North Sulawesi) | 🇮🇩 🇵🇭 | | 2GO Travel | | year round |
| Davao to General Santos | 🇵🇭 🇵🇭 | 9h | 2GO Travel | 2 | year round |
| Dili to Atauro | 🇹🇱 🇹🇱 | 2h to 3h | APORTIL | | seasonal |
| Dili to Oecusse (Pante Macassar) | 🇹🇱 🇹🇱 | 12h | APORTIL | | seasonal |
| Dipolog to Zamboanga | 🇵🇭 🇵🇭 | 11h | 2GO Travel | 1 | year round |
| Don Sak to Koh Phangan (Thong Sala) | 🇹🇭 🇹🇭 | 1h 45m to 2h 30m | 3 operators | 84 | year round |
| Don Sak to Koh Samui (Lipa Noi) | 🇹🇭 🇹🇭 | 1h 30m | Raja Ferry Port | 84 | year round |
| Don Sak to Koh Samui (Nathon) | 🇹🇭 🇹🇭 | 1h to 1h 30m | Seatran Ferry, Lomprayah | 70 | year round |
| Dumaguete to Dapitan | 🇵🇭 🇵🇭 | 4h to 6h | 5 operators | 49 | year round |
| Dumaguete to Dipolog | 🇵🇭 🇵🇭 | 3h 30m to 6h | 3 operators | 15 | year round |
| Dumaguete to Siquijor | 🇵🇭 🇵🇭 | 40m to 2h | 3 operators | 35 | year round |
| Dumaguete to Tagbilaran | 🇵🇭 🇵🇭 | 2h | OceanJet | 14 | year round |
| Dumaguete to Zamboanga | 🇵🇭 🇵🇭 | 16h 30m | 2GO Travel | 1 | year round |
| Dumai to Melaka | 🇮🇩 🇲🇾 | 2h to 3h | Indomal Fast Ferry, Tunas Rupat | 14 | year round |
| Dumangas (Iloilo) to Banago (Bacolod) | 🇵🇭 🇵🇭 | 1h | FastCat, Starlite Ferries | 28 | year round |
| Ende to Kupang | 🇮🇩 🇮🇩 | | Pelni | | year round |
| General Santos to Bitung (North Sulawesi) | 🇮🇩 🇵🇭 | | 2GO Travel | | year round |
| General Santos to Iloilo | 🇵🇭 🇵🇭 | 25h | 2GO Travel | 1 | year round |
| Ha Tien to Phu Quoc (Bai Vong) | 🇻🇳 🇻🇳 | 1h 30m to 3h | 3 operators | | ~Nov-Apr |
| Hai Phong (Ben Binh) to Cat Ba Town | 🇻🇳 🇻🇳 | 45m to 1h | Cat Ba Express | | year round |
| Iligan to Ozamiz | 🇵🇭 🇵🇭 | 2h | Cokaliong Shipping Lines, Trans-Asia Shipping Lines | 6 | year round |
| Iloilo to Puerto Princesa | 🇵🇭 🇵🇭 | 36h | Montenegro Shipping Lines | 1 | year round |
| Jagna (Bohol) to Nasipit (Butuan) | 🇵🇭 🇵🇭 | 8h to 12h | Lite Ferries, Cokaliong Shipping Lines | 6 | year round |
| Jakarta to Batam | 🇮🇩 🇮🇩 | 32h | Pelni | 1 | year round |
| Jakarta to Kijang (Bintan) | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Jakarta to Pontianak | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Jakarta to Surabaya | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Johor Bahru to Batam Centre | 🇮🇩 🇲🇾 | | Dolphin Ferry, Pintas Fast Ferry | | year round |
| Johor Bahru to Batam Harbour Bay | 🇮🇩 🇲🇾 | | Bistari Gemilang Travel | 35 | year round |
| Johor Bahru to Gold Coast Bengkong | 🇮🇩 🇲🇾 | | Dolphin Ferry | 21 | year round |
| Kayangan to Poto Tano | 🇮🇩 🇮🇩 | | ASDP Indonesia Ferry, Jembatan Nusantara | | year round |
| Ketapang to Gilimanuk | 🇮🇩 🇮🇩 | 45m to 1h | ASDP Indonesia Ferry, Jembatan Nusantara | | year round |
| Koh Lanta to Koh Phi Phi | 🇹🇭 🇹🇭 | 30m to 1h | Bundhaya Speed Boat, Tiger Line Ferry | | ~Oct-May |
| Koh Lipe to Koh Lanta | 🇹🇭 🇹🇭 | 3h to 5h | Tiger Line Ferry, Satun Pakbara Speed Boat Club | | ~Nov-Apr |
| Koh Lipe to Koh Phi Phi | 🇹🇭 🇹🇭 | 4h to 6h | Satun Pakbara Speed Boat Club | | ~Oct-May |
| Koh Phangan to Koh Tao | 🇹🇭 🇹🇭 | 1h to 1h 30m | 3 operators | | year round |
| Koh Samui (Bangrak) to Koh Phangan | 🇹🇭 🇹🇭 | 20m to 45m | Seatran Discovery, Songserm | | year round |
| Koh Samui (Bangrak) to Koh Tao | 🇹🇭 🇹🇭 | 1h 45m to 2h 15m | Seatran Discovery, Songserm | | year round |
| Koh Samui (Maenam) to Koh Phangan | 🇹🇭 🇹🇭 | 30m | Lomprayah | | year round |
| Koh Samui (Maenam) to Koh Tao | 🇹🇭 🇹🇭 | 1h 30m to 1h 45m | Lomprayah | | year round |
| Kota Kinabalu to Labuan | 🇲🇾 🇲🇾 | 3h to 3h 30m | Labuan Express | 7 | year round |
| Krabi to Koh Lanta | 🇹🇭 🇹🇭 | 1h 10m to 1h 30m | Andaman Wave Master, Satun Pakbara Speed Boat Club | | ~Nov-Apr |
| Krabi to Koh Phi Phi | 🇹🇭 🇹🇭 | 1h to 1h 30m | Andaman Wave Master, Chaokoh Ferry | | ~Nov-Apr |
| Kuala Besut to Perhentian Besar | 🇲🇾 🇲🇾 | 30m to 45m | Perhentian Boat Services, Perhentian Trans Holidays | | ~Mar-Oct |
| Kuala Besut to Perhentian Kecil | 🇲🇾 🇲🇾 | 30m to 45m | Perhentian Boat Services | | ~Mar-Oct |
| Kuala Kedah to Langkawi | 🇲🇾 🇲🇾 | 1h 45m to 2h | Langkawi Ferry Line | | year round |
| Kuala Perlis to Langkawi | 🇲🇾 🇲🇾 | 1h 15m to 1h 30m | Langkawi Ferry Line | | year round |
| Kudat to Pulau Banggi | 🇲🇾 🇲🇾 | 2h to 2h 30m | Kudat Ferries Service | 7 | year round |
| Labuan Bajo to Makassar | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Labuan to Lawas | 🇲🇾 🇲🇾 | 2h to 2h 30m | Ratu Pertama | | year round |
| Labuan to Limbang | 🇲🇾 🇲🇾 | 2h to 2h 30m | Pertama Limbang, Royal Limbang | 14 | year round |
| Laem Sok (Trat) to Koh Kut | 🇹🇭 🇹🇭 | 1h 10m to 1h 30m | Boonsiri High Speed Catamaran | | ~Nov-May |
| Laem Sok (Trat) to Koh Mak | 🇹🇭 🇹🇭 | 50m to 1h | Boonsiri High Speed Catamaran | | ~Nov-May |
| Langkawi (Kuah) to Koh Lipe | 🇹🇭 🇲🇾 | 1h 30m to 4h | Satun Pakbara Speed Boat Club | | ~Oct-May |
| Langkawi (Telaga Harbour) to Koh Lipe | 🇹🇭 🇲🇾 | 1h 30m to 4h | Bundhaya Speed Boat | | ~Oct-May |
| Langkawi to Satun (Tammalang) | 🇲🇾 🇹🇭 | 1h 15m to 1h 30m | Langkawi Ferry Line | 28 | year round |
| Lembar to Bima (Sumbawa) | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Liloan (Southern Leyte) to Lipata (Surigao) | 🇵🇭 🇵🇭 | 3h to 3h 30m | Montenegro Shipping Lines | 21 | year round |
| Lumut to Pangkor | 🇲🇾 🇲🇾 | 30m to 45m | Pangkor Ferry | 147 | year round |
| Lumut to Sungai Pinang Kecil (Pangkor) | 🇲🇾 🇲🇾 | 20m to 30m | Pangkor Ferry | 147 | year round |
| Maasin (Southern Leyte) to Surigao | 🇵🇭 🇵🇭 | 2h to 4h | OceanJet, FastCat | 14 | year round |
| Makassar to Baubau | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Makassar to Maumere | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Makassar to Pare-Pare | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Manila (Pasay) to Puerto Princesa | 🇵🇭 🇵🇭 | 17h | 2GO Travel | 1 | year round |
| Manila to Bacolod | 🇵🇭 🇵🇭 | 21h | 2GO Travel | 3 | year round |
| Manila to Butuan (Masao) | 🇵🇭 🇵🇭 | 44h | 2GO Travel | 1 | year round |
| Manila to Cagayan de Oro | 🇵🇭 🇵🇭 | 39h | 2GO Travel | 2 | year round |
| Manila to Cebu | 🇵🇭 🇵🇭 | 24h | 2GO Travel | 2 | year round |
| Manila to Coron | 🇵🇭 🇵🇭 | 13h | 2GO Travel | 1 | year round |
| Manila to Davao | 🇵🇭 🇵🇭 | 61h | 2GO Travel | 2 | year round |
| Manila to Dipolog | 🇵🇭 🇵🇭 | 49h 30m | 2GO Travel | 1 | year round |
| Manila to Dumaguete | 🇵🇭 🇵🇭 | 55h | 2GO Travel | 1 | year round |
| Manila to General Santos | 🇵🇭 🇵🇭 | 48h | 2GO Travel | 1 | year round |
| Manila to Iloilo | 🇵🇭 🇵🇭 | 30h | 2GO Travel | 3 | year round |
| Manila to Ozamiz | 🇵🇭 🇵🇭 | 44h | 2GO Travel | 1 | year round |
| Manila to Tagbilaran | 🇵🇭 🇵🇭 | 33h | 2GO Travel | 1 | year round |
| Manila to Zamboanga | 🇵🇭 🇵🇭 | 48h 30m | 2GO Travel | 1 | year round |
| Marina Island to Pangkor | 🇲🇾 🇲🇾 | 10m to 15m | Pangkor Ferry | | year round |
| Matnog to Allen | 🇵🇭 🇵🇭 | 2h | 3 operators | 126 | year round |
| Matnog to Dapdap (San Isidro, Samar) | 🇵🇭 🇵🇭 | 1h 30m | FastCat | 14 | year round |
| Merang to Redang | 🇲🇾 🇲🇾 | 30m to 45m | Al Ameen Boat Service, Vigourmarine Transtour | 70 | ~Mar-Oct |
| Mersing to Tioman (Kampung Genting) | 🇲🇾 🇲🇾 | 1h 30m to 2h | Bluewater Express | 21 | ~Mar-Oct |
| Mersing to Tioman (Tekek) | 🇲🇾 🇲🇾 | 1h 30m to 2h | Bluewater Express | 21 | ~Mar-Oct |
| Padangbai to Bangsal | 🇮🇩 🇮🇩 | | 3 operators | 42 | ~Apr-Oct |
| Padangbai to Gili Air | 🇮🇩 🇮🇩 | | 3 operators | 42 | ~Apr-Oct |
| Padangbai to Gili Meno | 🇮🇩 🇮🇩 | | Eka Jaya Fast Ferry, Semaya One | | ~Apr-Oct |
| Padangbai to Gili Trawangan | 🇮🇩 🇮🇩 | 1h 30m to 2h 40m | 7 operators | 56 | ~Apr-Oct |
| Padangbai to Lembar | 🇮🇩 🇮🇩 | 4h to 5h | 3 operators | 98 | year round |
| Padangbai to Senggigi | 🇮🇩 🇮🇩 | | Golden Queen Fast Boat, Eka Jaya Fast Ferry | 7 | ~Apr-Oct |
| Pak Bara to Koh Lipe | 🇹🇭 🇹🇭 | 1h 30m | Bundhaya Speed Boat | 21 | ~Oct-May |
| Pare-Pare to Balikpapan | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Phuket to Koh Lanta | 🇹🇭 🇹🇭 | 1h 30m to 2h 30m | Andaman Wave Master, Tiger Line Ferry | | ~Nov-Apr |
| Phuket to Koh Phi Phi | 🇹🇭 🇹🇭 | 1h to 2h | Andaman Wave Master, Chaokoh Ferry | | ~Nov-Apr |
| Phuket to Krabi | 🇹🇭 🇹🇭 | 2h to 7h | 3 operators | 34 | year round |
| Pontianak to Semarang | 🇮🇩 🇮🇩 | | Pelni, Dharma Lautan Utama | | year round |
| Pontianak to Surabaya | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Rach Gia to Phu Quoc (Bai Vong) | 🇻🇳 🇻🇳 | 2h 30m to 3h 30m | 3 operators | | ~Nov-Apr |
| Sampit to Semarang | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Sanur to Gili Trawangan | 🇮🇩 🇮🇩 | | Scoot Fast Cruises, Wijaya Perkasa | | ~Apr-Oct |
| Sanur to Nusa Lembongan (Jungut Batu) | 🇮🇩 🇮🇩 | 30m to 40m | 3 operators | | ~Apr-Oct |
| Sanur to Nusa Penida (Toya Pakeh) | 🇮🇩 🇮🇩 | 30m to 35m | El Rey Junior, Wijaya Perkasa | 21 | ~Apr-Oct |
| Sanur to Senggigi | 🇮🇩 🇮🇩 | | Scoot Fast Cruises | | ~Apr-Oct |
| Semarang to Kumai | 🇮🇩 🇮🇩 | | Pelni, Dharma Lautan Utama | | year round |
| Serangan to Gili Trawangan | 🇮🇩 🇮🇩 | 3h to 4h | Marina Srikandi, Gili Getaway | 7 | ~Apr-Oct |
| Sihanoukville to Koh Rong (Koh Touch) | 🇰🇭 🇰🇭 | 30m to 50m | 4 operators | 21 | seasonal |
| Sihanoukville to Koh Rong Sanloem (Saracen Bay) | 🇰🇭 🇰🇭 | 30m to 50m | 4 operators | | seasonal |
| Singapore (Changi Point) to Tanjung Belungkor | 🇸🇬 🇲🇾 | 30m to 45m | Limbongan Maju | 24 | year round |
| Singapore HarbourFront to Batam Centre | 🇮🇩 🇸🇬 | 1h to 1h 15m | 3 operators | 259 | year round |
| Singapore HarbourFront to Gold Coast Bengkong | 🇮🇩 🇸🇬 | | Batam Fast Ferry, Sindo Ferry | 35 | year round |
| Singapore HarbourFront to Sekupang | 🇮🇩 🇸🇬 | 45m to 1h | 3 operators | 161 | year round |
| Singapore HarbourFront to Tanjung Balai Karimun | 🇸🇬 🇮🇩 | | Sindo Ferry | 14 | year round |
| Singapore HarbourFront to Waterfront City | 🇮🇩 🇸🇬 | | Sindo Ferry | 14 | year round |
| Singapore Tanah Merah to Bandar Bentan Telani | 🇮🇩 🇸🇬 | | Bintan Resort Ferries | 59 | year round |
| Singapore Tanah Merah to Batam Centre | 🇮🇩 🇸🇬 | | 3 operators | 111 | year round |
| Singapore Tanah Merah to Nongsapura | 🇮🇩 🇸🇬 | | Batam Fast Ferry | 56 | year round |
| Singapore Tanah Merah to Tanjung Pinang | 🇸🇬 🇮🇩 | | Sindo Ferry, Majestic Fast Ferry | 28 | year round |
| Soc Trang (Tran De) to Con Dao | 🇻🇳 🇻🇳 | 2h to 2h 30m | Superdong, Con Dao Express | 14 | ~Nov-Apr |
| Surabaya to Balikpapan | 🇮🇩 🇮🇩 | | Pelni, Dharma Lautan Utama | | year round |
| Surabaya to Banjarmasin | 🇮🇩 🇮🇩 | 19h to 20h | Dharma Lautan Utama | | year round |
| Surabaya to Batulicin | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Surabaya to Benoa (Bali) | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Surabaya to Kumai | 🇮🇩 🇮🇩 | | Pelni, Dharma Lautan Utama | | year round |
| Surabaya to Makassar | 🇮🇩 🇮🇩 | | Pelni, Dharma Lautan Utama | | year round |
| Surabaya to Sampit | 🇮🇩 🇮🇩 | | Dharma Lautan Utama | | year round |
| Surat Thani (Tapee Pier) to Koh Phangan | 🇹🇭 🇹🇭 | 4h to 5h | Raja Ferry Port | | year round |
| Surat Thani (Tapee Pier) to Koh Samui | 🇹🇭 🇹🇭 | 2h 30m to 3h | Lomprayah | | year round |
| Surigao to Dapa (Siargao) | 🇵🇭 🇵🇭 | 2h | Montenegro Shipping Lines | 14 | year round |
| Tagbilaran to Cagayan de Oro | 🇵🇭 🇵🇭 | 10h 30m to 11h 30m | Lite Ferries, Trans-Asia Shipping Lines | 6 | year round |
| Tanjung Balai Karimun to Belawan | 🇮🇩 🇮🇩 | 23h | Pelni | 2 | year round |
| Tanjung Gemok to Tioman (Kampung Genting) | 🇲🇾 🇲🇾 | 1h 30m to 2h | Bluewater Express | 21 | ~Mar-Oct |
| Tanjung Gemok to Tioman (Tekek) | 🇲🇾 🇲🇾 | 1h 30m to 2h | Bluewater Express | 21 | ~Mar-Oct |
| Tarakan to Nunukan | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Toledo (Cebu) to San Carlos (Negros) | 🇵🇭 🇵🇭 | 1h 30m to 2h | FastCat, Lite Ferries | 21 | year round |
| Vung Tau to Con Dao | 🇻🇳 🇻🇳 | 3h 45m to 4h 15m | Phu Quoc Express | | ~Nov-Apr |
| Waingapu to Ende | 🇮🇩 🇮🇩 | | Pelni | | year round |
| Zamboanga to Bongao (Tawi-Tawi) | 🇵🇭 🇵🇭 | 17h | Aleson Shipping Lines, Montenegro Shipping Lines | 4 | year round |
| Zamboanga to Isabela (Basilan) | 🇵🇭 🇵🇭 | 1h to 1h 30m | 4 operators | 56 | year round |
| Zamboanga to Jolo (Sulu) | 🇵🇭 🇵🇭 | 3h 30m to 9h | 3 operators | 18 | year round |
| Zamboanga to Lamitan (Basilan) | 🇵🇭 🇵🇭 | 1h 30m to 2h | Montenegro Shipping Lines, Aleson Shipping Lines | 14 | year round |
| Zamboanga to Sandakan (Sabah) | 🇲🇾 🇵🇭 | 16h | Aleson Shipping Lines | 1 | year round |
