The main international airports in Indonesia are Bali (DPS) and Jakarta (CGK) and from both of these there are daily flights to Labuan Bajo, although Bali - Labuan flights are much more frequent.
Air Asia and Jetstar are offering direct flights from Kuala Lumpur to Labuan Bajo!
International Arrivals Into Bali Denpasar (DPS)
Visa on Arrival is available for citizens of 86 countries. The visa costs Rp 500,000 (approx. USD35 / SGD or AUD50 / GBP27 / EUR32 / MYR145), it's valid for 30 days and can be extended once for a further 30 days. You can apply for this up to 14 days in advance online at: https://evisa.imigrasi.go.id/.
Citizens of 15 countries are eligible for the Visa Exemption (read more here).
Foreign travellers from countries other than the 86 listed countries must first apply for a B211A Tourist Visa prior to entering Bali.
All visitors to Indonesia need at least 6 months passport validity.
For a list of the full requirements please visit Welcome Back To Bali
Tourism Levy for International Arrivals Into Bali Denpasar (DPS)
International arrivals to Bali will be required to pay a one-time Rp 150,000 (approx. US$10) fee.
Travellers are encouraged to conveniently settle this payment via the Love Bali website or App prior to their arrival. Upon payment, a tourism levy voucher will be sent via email, and tourists should store it on their smartphones for scanning at checkpoints in Bali Airport and sea ports.
"All Indonesia"
Indonesia has introduced a unified digital portal named “All Indonesia”, to streamline immigration, customs, and health procedures into a single form which can be filled out 72 hours before your arrival.