Malaysian authorities have rescued 46 Indonesians who were trying to sneak back into their country when their boat sank, an official said Wednesday.

The 46 men, all believed to be illegal immigrants, were saved from the rickety boat after it experienced engine trouble off southern Johor state early Tuesday, a Malaysian Maritime Enforcement Agency official said.

"The engine had a problem, and the boat sank," he told AFP. "It happened in rough weather."

The official said the boat sent a distress call but maritime officials took 10 hours to locate it, arriving just before it sank.

The immigrants were taken into custody pending further investigations, but the skipper managed to escape before the boat sank, the official said. The boat was headed to Indonesia's Batam island, he said.

Hundreds of illegal immigrants from neighbouring Indonesia have been arrested off southern Malaysia this year alone for trying to sneak in or out of the country, where they seek work on construction sites and other places.

Last month, seven Indonesians went missing and 17 others were rescued after their boat capsized off Johor state.

About 1.1 million Indonesian work legally in Malaysia, while another 900,000 are estimated to live in the more prosperous nation illegally. Many return to Indonesia for the Muslim fasting month of Ramadan, which begins in August.