A nation of 17,000 islands and more than 70 languages, Indonesia spans three time zones and is home to nearly 150 active volcanoes. Its wildlife is diverse too, representing South-East Asia and Australasia, but thanks to the Wallace Line – a “faunal boundary” that cuts across the country – nowhere do these different creatures mix.
Cruising, however, allows you to cross this boundary with ease, which adds to the fascination of discovering this destination by sea. What’s more, after being badly affected by floods in late 2025, tourism is now especially important for Indonesia’s economic recovery.
Although cruises operate year-round, Indonesia is seasonal. Raja Ampat and the Maluku (or Spice) Islands are best visited during the monsoon season, typically from October to April. Outside of this time (i.e, from April until October), conditions are optimal for the Komodo Islands.
I’ve been fortunate enough to sail here, pausing to swim with whale sharks, visit pink-sand beaches and watch hundreds of fruit bats stream across the evening sky. So if your bucket list features Komodo dragons, snorkelling over coral gardens or even spotting orangutans, prepare to tick them off on one of these Indonesia cruises.
Find by cruise type:
Best for wildlife spotting
Bali & Komodo National Park
Aqua Expeditions
Key stops: Moyo Island, Komodo Island, Saleh Bay (Sumbawa), Gili Lawa and Padar Islands
Departure port: Benoa for Bali
Duration: Seven nights
Ship: Aqua Blu
The Komodo archipelago is the most iconic port of call for any cruise in Indonesian waters. After all, this is the only place to see Komodo dragons, the world’s largest lizard species, in the wild. When I visited, I saw these living dinosaurs at thrillingly close quarters. But the islands have other headline attractions in store, such as the hilltop viewpoint on Padar Island and flamingo-hued sands of Pink Beach on Komodo Island.
Throughout the Komodo season (which runs from April to September), Aqua Expeditions’ luxurious 15-suite ship Aqua Blu shuttles between Bali and Flores on seven-night sailings that include visits to local villages, a waterfall swim on Moyo Island and the chance to go diving (included in the price) or snorkelling almost daily. The well-paced, action-packed itinerary is meticulously planned.
Insider tip
For the utmost privacy and best views, book suites 401 or 402 (or both: they’re interconnecting) to be the only guests staying on the ship’s bridge deck.
How to do it
A seven-night Bali and Komodo National Park itinerary departing on May 9, 2026, costs from £7,800pp for a Category III cabin. Includes twice daily excursions with expert guides, watersports equipment and Wi-Fi. Excludes flights.
Best for exclusivity
Raja Ampat Conservation Voyage
Rascal Voyages
Key stops: Raja Ampat: Dampier Strait (Friwinbonda Island), Mansuar Island, Arborek, Wayag Islands, West Waigeo, Wofoh Island, Penemu Island, Yefnabi and Yeben
Departure port: Sorong
Duration: Seven nights
Ship: Rascal or Rebel
Indonesia’s other cruise big-hitter is Raja Ampat: a wild archipelago of coral cays, fish-rich reefs and jungle-clad isles. The best time to visit is from mid-December to March, when there is a chance to see nesting sea turtles and migrating mantas, and visibility for diving and snorkelling is at its best.
Rascal Voyages blends comfort, curiosity and conservation aboard either its two, five-cabin yachts, Rascal and Rebel (which can also be hired exclusively).
Sorong, the departure point, is reached by air from Bali, Jakarta or Singapore, and the line’s concierge team manages every step of the onward journey from the moment guests land. As well as on-the-ground experiences such as spotting birds of paradise, guests can look forward to snorkelling over pristine coral and exploring a truly off-grid part of the world.
Insider tip
Rascal Voyages’ collaboration with Dr Calvin Beale of the Manta Trust supports tagging, research and manta-monitoring in the Dampier Strait. Be sure to attend onboard briefings when visiting here on a Conservation Voyage to learn about these cutting-edge studies.
How to do it
A seven-night Raja Ampat Conservation Voyage departing on November 15, 2026, costs from £2,605pp for a Master cabin. Includes excursions. Excludes flights. (rascalvoyages.com).
Best for a bucket-list voyage
Corals and Cultures of Indonesia
Noble Caledonia
Key stops: Satonda Island, Komodo Island, Taka Bonerate National Park, Banda Islands, Wakatobi National Marine Park, Padaido Islands, Raja Ampat and Jayapura (Indonesia), Wewak, Garove Island and Rabaul (Papua New Guinea), Singapore
Departure port: Benoa, Bali
Duration: 19 nights
Ship: MS Island Sky
No worries if you can’t decide between a Komodo or Raja Ampat itinerary: this trip with Noble Caledonia ticks off both on its 16-night cruise between Bali and Papua New Guinea.
The 118-passenger Island Sky sails through some of the world’s least-visited waters and marine parks, exposing passengers to outstanding natural beauty. Snorkelling, Komodo dragons, birds of paradise and visits to empty beaches and remote villages fill each portion of the journey with wonder and intrigue. There is also a final foray to the island of New Guinea, covering both Indonesian West Papua and Papua New Guinea across the border.
The 59-cabin MS Island Sky is spacious and comfortable, and the polished mahogany and brass interiors give it the air of a traditional yacht.
Insider tip
For a more luxurious stay, choose the impressive Island Suite (located on the Explorer Deck) for its extra-large balcony that stretches the full length of the suite.
How to do it
A 19-night Corals and Cultures of Indonesia cruise departing August 22, 2026, costs from £11,995pp for a Magellan deck standard suite. Includes flights, transfers, overnight hotel accommodation in both Bali and Singapore (with breakfast), shore excursions and tips.
Best for an off-grid adventure
Rare Species, Remote Cultures and Remarkable Corals with Dr George Beccaloni
SeaTrek Sailing Adventures
Key stops: Maluku Islands, Guraici Archipelago, Bacan Island, Banggai, Obi Latu, Togean Islands National Park, Sulu Archipelago, Taliabu Island, Bokan Islands, Bitung for Bali
Departure port: Ternate, North Maluku
Duration: 13 nights
Ship: Ombak Putih
For authenticity, nothing beats sailing these waters on a traditional wooden pinisi boat. Built by the seafaring peoples of Sulawesi, these hand-crafted, gaff-rigged boats are part of Indonesia’s cultural heritage. SeaTrek’s two vessels have been outfitted with the latest technology as well as tenders, kayaks, paddleboards and snorkelling gear.
This particular itinerary focuses on Sulawesi and its satellite islands. Black-crested macaques, babirusas (wild pigs) and golden birdwings, the world’s largest butterflies, are among the potential wildlife spots, as is the chance to snorkel with whale sharks and colourful, stingless jellyfish.
SeaTrek’s trips are transformative experiences that go well off the beaten path. In keeping with this ethos, the company supports conservation and community initiatives, and its entire operation is carbon neutral.
Insider tip
Consider extending any SeaTrek cruise with a side-trip to Kalimantan, the Indonesian division of Borneo, to see orangutans in their natural habitat.
How to do it
A 13-night Rare Species, Remote Cultures and Remarkable Corals cruise departing on February 23, 2027, costs from £8,280pp. Excludes flights and fuel surcharge (seatrekbali.com).
Best for learning about Indigenous cultures
Island Empires and Ancient Mariners
Coral Expeditions
Key stops: Sulawesi, Komodo Island, West Timor, Alor Island, Kelimutu National Park, Padar Island, Jailamu Island, Sagori, Sulawesi Island
Departure port: Darwin (Australia)
Duration: 14 nights
Ship: Coral Geographer
One of the things that makes Indonesia so special is its range of cultures and traditional communities spread across the archipelago. This Coral Expeditions cruise visits the small and rugged Alor Island, whose 140,000 inhabitants speak more than 50 different languages. In Sulawesi, you can watch traditional pinisi boats being built on the beach and stay overnight in a mountain village.
There are plenty of chances for wildlife encounters too, with Komodo dragons on land and sea turtles in the water, plus crater lakes and views over sweeping coves whose beaches have white, pink and dark-coloured sands.
You’ll be sailing aboard the purpose-built Coral Geographer, whose full complement stretches to just 120 guests and 46 crew: a factor that contributes to making the voyage both intimate and amazing. Off-ship experiences are conducted on either Zodiacs or Xplorer craft, so even guests with impaired mobility need not miss out on any adventures.
Insider tip
Remember to have local currency to hand when visiting the talented weavers of Lamalera village, whose ikat textile creations make marvellous souvenirs (and purchases directly benefit this isolated community).
How to do it
A 14-night The Island Empires and Ancient Mariners voyage departing on November 28, 2026, costs from £10,647pp for a Coral deck cabin. Includes 13 nights on board and one night in local accommodation mid-cruise, drinks with meals, Wi-Fi, tips and shore excursions. (coralexpeditions.com)
Best for affordability
Singapore & Indonesia: Senarang, Surabaya & Bali
Azamara Cruises
Key stops: Semarang and Surabaya (Java), Celukan Bawang and Benoa (Bali)
Departure port: Singapore
Duration: Seven nights
Ship: Azamara Pursuit
Larger ships are not able to offer the same level of hands-on adventure that you might find on an expedition cruise, but their economies of scale make fares significantly lower. Although this seven-night Azamara sailing on the 702-passenger Azamara Pursuit is limited to more commercial ports and destinations, it nevertheless dips into some of Indonesia’s diverse local cultures on its journey from Singapore to Bali.
The first day after leaving the shores of the Lion City is spent at sea, enjoying the ship’s facilities like relaxing in the Sanctum Spa or watching a performance in the Cabaret Lounge. Then there are two stops on Java, to the cities of Semarang and Surabaya, where temples sit alongside Arabic-influenced stalls selling perfumes, prayer beads and dates. Finally, a day is spent in Bali’s Celukan Bawang, a picturesque port in the north of the island, before docking and disembarking in Benoa.
Insider tip
For a quiet moment onboard, seek out The Den: a chilled-out space stocked with books designed to fire your wanderlust.
How to do it
A seven-night Bali, Surabaya, and Semarang cruise departing on October 16, 2027, costs from £1,819pp for an interior cabin. Includes dining, drinks and gratuities.
About our expert
James Litston
James is a freelance travel writer from the UK. His special interest in wildlife, adventure and expedition cruises has taken him all over the world, from Australia to South Africa, Northern Europe to the Mediterranean.