At least nine people were killed and dozens more are missing after a string of boats capsized in a storm that battered Indonesia's section of Borneo island, a local rescue agency said Friday.

The accident happened early Wednesday in waters off the coast of West Kalimantan where waves as high as five metres (16 feet) swamped a dozen fishing vessels and pair of tugboats.

It was first reported by search-and-rescue authorities on Friday.

Nine people have been confirmed dead with another 46 still missing, said Yopi Haryadi, head of the Pontianak rescue agency, who added that 81 people on the vessels had been rescued alive.

The storm inundated nearly 50 villages on land, destroying homes and other buildings with nearly 15,000 residents affected.

"The 14 boats actually tried to escape from the storm but it was too strong and they capsized," Haryadi told AFP.

"The storm also battered the mainland in West Kalimantan where villages were inundated by floods. But there are no casualties or people missing so far on the mainland."

The local search and rescue agency said a military helicopter was deployed to help in the hunt for any survivors, but the operation was being hampered by bad weather.

"Hopefully the weather today will be good so we can find other victims," said Eryk Subarianto, chief of emergency operations at the Pontianak rescue agency.

Marine accidents are common in Indonesia, a Southeast Asian archipelago of more than 17,000 islands where many use ferries and other boats to travel despite poor safety standards.

Last month, a passenger ferry sank off the coast of holiday island Bali in rough seas, leaving 10 people dead with another still missing.

In 2018, about 160 people drowned when a ferry sank in one of the world's deepest lakes on Sumatra island.

And more than 300 people are estimated to have drowned in 2009 when a ferry sank between Sulawesi and Borneo.