Gunmen kidnapped three Indonesian members of a tugboat crew off Malaysia's eastern state of Sabah, police said on Sunday, the latest in a string of abductions in a region noted for kidnappings by Islamist militants.

It was not immediately clear whether the men were seized by Abu Sayyaf, a group linked to Islamic State that is responsible for recent beheadings of Western hostages and notorious for the extortion of millions of dollars in ransoms.

The tugboat, with a crew of seven, was in waters off the east coast of Sabah on Borneo island, about 3.6 nautical miles from a nearby Kampung Sinakut beach, Sabah police commissioner Abdul Rashid Harun said, when it was attacked by armed men in a white boat late on Saturday.

He said that based on early investigations, the three men kidnapped were 34-year-old Lorens Koten, 40-year-old Teo Dores Kopong and a 46-year-old identified only as Emanuel.

Abdul Rashid said they are likely to be in the southern Philippines now but did not elaborate. Four other crew members were left behind by the kidnappers who came in a speedboat.

"Victims released also said while the kidnappers were on their tugboat for nearly 30 minutes, no violence took place," he told reporters at a press conference in Lahad Datu.

The five abductors were armed with rifles and also had a grenade launcher, the police added.

In Jakarta, the Indonesian foreign ministry said it had no information yet on the abductions.

The Abu Sayyaf militant group has beheaded two Canadian nationals recently after its ransom deadlines expired. It is still holding men from Japan, the Netherlands and Norway.