The three fishermen, who were kidnapped by suspected seven-member Filipino armed group off Sabah's east coast, have been taken to the Abu Sayyaf hideout in southern Philippines.
Reports said the three fishermen are being held at gunpoint under the command of notorious Abu Sayyaf leader Majan Sahidjuan, also known as Apo Mike.
Five other Malaysian tugboat crewmen who were abducted on July 8 in waters off Dent Haven in Lahad Datu are also supposed to be under Apo Mike.
Abdul Rashid Harun, the Sabah Police Commissioner, said that they received a call from a foreign number soon after the three fishermen were kidnapped. He said the police were trying to verify the call, but refused to reveal the contents of the telephonic conversation.
Rashid identified the three fishermen as Masurin Jamalan, Sami Ghani and Loloi Alpin. He also said that as far as they were aware, three of them were safe.
The three kidnapped fishermen are Filipino migrants and were holding Immigration Department's IMM13 document, which allows them to reside and work in Sabah.
They are believed to be among a crew of 11 on the boat when the 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.
Soon after the abduction, 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 of ruthless kidnappers in recent times.
Earlier this year, the militants beheaded two Canadians whom they had kidnapped from a beach resort after a ransom deadline passed.
Recently, Philippine President Rodrigo Duterte warned the Abu Sayyaf group that he would eat them "alive" as they were "beyond redemption."