Four abducted Sarawakians freed by by Abu Sayyaf
Malaysian marine police boat on patrol near Semporna Reuters (Representational Image)

Three fishermen have been kidnapped by suspected seven-member Filipino armed group in Sabah waters near the tourist resort of Pulau Pom Pom off Semporna on late Saturday.

Authorities believe that the victims have been taken across the border towards the southern Philippines island chain of Tawi Tawi province.

Eastern Sabah Security Command (Esscom) commander Abdul Bari Abdul Khalid said they were informed by the owners of the fishing trawler at 1:59 am on Sunday.

"I can only confirm. Sabah police commissioner (Abdul Rashid Harun) will release the details later," he told The Star Online.

The owner of the fishing boat confirmed that the skipper and two crew members were kidnapped by the gunmen at about 10:20 pm on Saturday.

The three fishermen who have been identified as Flipino Bajaus are believed to be among a crew of 11 on the boat when seven kidnappers confronted them at gunpoint.

The kidnappers took only three crewmen while the rest of the crew steered the trawler back to the Semporna jetty. The witnesses said the gunmen fled in a green-coloured fast boat towards southern Philippines with those three fishermen.

This comes two days after Esscom conducted as intensive operations against cross-border smugglers in the five districts in the east coast.

Esscom said the security forces were on high alert along the border while the Philippines military troops launched a massive all-out war against the Abu Sayyaf militants in Jolo.

The Abu Sayyaf group which is linked to the Islamic State in Iraq and Syria (ISIS) have been responsible for a series of abductions and have developed a reputation as ruthless kidnappers in recent times.

The Abu Sayyaf militants beheaded two Canadians whom they had kidnapped from a beach resort after a ransom deadline passed.

Philippine President Rodrigo Duterte warned the Abu Sayyaf group recently that he would eat them "alive" as they were "beyond redemption."

The rise of kidnapping incidents at sea has prompted Indonesia, the Philippines and Malaysia governments to try to coordinate maritime patrols in order to control such incidents.