Air
Several domestic airlines offer regular flights between Denpasar, Bali and Labuan Bajo, Ende or Maumere. Flights also operate between Maumere and Kupang, West Timor. Find and book flights online with tiket.com or a reputable travel agent once you’re on the ground in Indonesia.
Land & Sea
This little used third option takes plenty of planning but it’s a good alternative for island hopping between Bali and Flores via Lombok and Sumbawa Islands. This option involves travelling across the islands via public transport or scooter and crossing between the islands using local boats or public ferries. Flexibility and a bit of time up your sleeve is the key to making this option work for you but it’s certainly a great way of seeing more of the islands.
Sea
Pelni (Indonesia’s national shipping company) operates passenger services between Bali and Labuan Bajo three times a month and Bali and Larantuka via Ende and Maumere once a month. With sea journeys taking between 1.5 – 3.5 days, travelling by ferry is really only suitable for those with plenty of time. If you’re doing a little island hopping, Pelni also connects Flores with other islands in the Lesser Sunda Island group and West Timor. Tickets can be purchased through any authorised Pelni agent. Check the Pelni website for routes, schedules and authorised agents.
Another popular alternative for travel between Labuan Bajo and Lombok, taking in various islands and attractions in the eastern Lesser Sunda Islands group, including the Komodo National Park, is a 3-4 day island cruise offered by several tour companies. There are some very affordable budget cruises as well as some top-end luxury cruises so most people will be able to find something to suit their budget.