At least two people are dead and 26 others are missing after a ferry carrying dozens of migrants sank off the coast of Indonesia, an official said Sunday. 

The wooden fishing boat was carrying 89 onboard when it departed for neighbouring Malaysia through an unguarded route. 

But it sprung a leak soon after departing before being hit by strong waves and sinking.

A man and a woman were found dead while 61 others were rescued and immediately transported to hospitals for treatment. The remaining passengers are still missing. 

"We have deployed our personnel to search for the 26 missing victims but our efforts haven't been fruitful so far," head of local search and rescue team Ady Pandawa told AFP on Sunday, adding that the damaged boat had been evacuated to the nearest port.

The passengers had come from across Indonesia and were seeking work in Malaysia without proper documentation, he added.

"We suspect the number of passengers exceeded the boat capacity so when the vessel was hit by strong waves, it immediately sank," he said.

Relatively affluent Malaysia is home to millions of migrants from poorer parts of Asia, many of them undocumented, working in industries including construction and agriculture.

Indonesians illegally seeking work in neighbouring Malaysia often risk dangerous sea crossings, and accidents are common due to bad weather and poor safety measures. 

In January six Indonesian women drowned off the coast of Malaysia after their boat capsized during a suspected attempt to enter the country illegally.

A month earlier, 21 Indonesian migrants also died after their boat capsized.