Thirty-two people are missing after an apparently overloaded boat carrying Indonesian migrants sank in rough waters off Malaysia's west coast.

Officials said 60 people were rescued or made it to land by themselves after the overnight accident near Port Klang, Malaysia's largest port.

Authorities have intensified their search operation with nine ships and a helicopter.

Rescued passengers said they were returning home to Indonesia across the Malacca Strait for the Muslim fasting month of Ramadan.

The Malacca Strait is a busy shipping lane between Malaysia and Indonesia's Sumatra island.

Officials had initially said the passengers were believed to be seeking to enter Malaysia.

"From interviews with those rescued, they said they were returning to Aceh [in northern Sumatra]. They did not have any travel documents," said Mohamad Hambali Yaakup, head of the Port Klang office of the Malaysian Maritime Enforcement Agency.

"As in previous years, many Indonesian migrants will be leaving Malaysia ahead of Ramadan."

The four men and one woman who died had drowned, he said.

"Rough seas are making our rescue operation difficult. But we will continue the search until the remaining 32 people are found," he added.

The boat sank not far from shore, raising hopes that many of the missing might make it to safety on their own.

Officials believe 97 passengers were aboard the wooden boat, including some children.