At least 13 people died after a boat carrying hundreds caught fire in eastern Indonesia on Monday, a transport official said.

The KM Express Cantika 77 erupted in flames off the coast of Timor island in East Nusa Tenggara province, prompting desperate passengers to jump overboard.

A search and rescue operation recovered 241 people alive out of 254 passengers and crew, Isyak Nuka, head of East Nusa Tenggara's transportation agency, told AFP.

"Thirteen people are dead. All 241 others are evacuated," Nuka said, without specifying the cause of the fire.

The head of a local search and rescue agency, I Putu Sudayana, gave a higher death toll of 14 and a lower passenger and crew count of 240.

"We have evacuated 240 people with 14 dead, 226 survived," he told AFP.

The boat's top deck set alight as it sailed from provincial capital Kupang to the town of Kalabahi on Alor island.

Authorities dispatched three rescue boats and local fishermen sailed out in their own boats to help the search effort.

Rescuers struggled to approach the ship because of the blaze and strong currents, Nuka said.

Some survivors will be treated in hospital for shock and the dead will be transferred to a police hospital in Kupang for identification, he said.

Many of those rescued had used life vests after the fire broke out and some swam directly to shore.

The boat had capacity for 250 people, the official said.

Marine accidents are common in the Southeast Asian archipelago of around 17,000 islands, where safety standards are often lax.

In 2018, more than 150 people drowned when a ferry sank in one of the world's deepest lakes on Sumatra island.