Gunmen on a speedboat have kidnapped four Malaysians from a ship off the east coast of Sabah state in waters where Abu Sayyaf militants are known to operate, the Malaysian government said Saturday.
Five other crew members including Myanmar and Indonesian nationals were released.
If the Philippine Islamist group is confirmed to be behind the kidnapping, it would be their second such hostage-taking in as many weeks and comes amid an uptick in such attacks.
"Malaysia strongly condemns the senseless and barbaric act," a foreign ministry statement said.
The ministry added it would work closely with Philippine authorities on investigations and towards securing the Malaysians' release.
Philippine regional army spokesman Felimon Tan said the military was verifying the reported kidnapping after Malaysian authorities informed them of the incident on Friday.
"Whether or not they were seized by the Abu Sayyaf or brought to the Philippines, we have yet to confirm," Tan told AFP.
Sabah police commissioner Abdul Rashid Harun told Malaysia's official news agency Bernama that authorities were still investigating if the kidnapping occurred in Malaysian or international waters.
"The area is vast and we have our assets there. So we are investigating whether it happened in or off our waters," he was quoted as saying by Bernama.
"The five other individuals in the ship comprising Myanmar and Indonesian nationals were released."
Malaysia's foreign ministry said the kidnapping occurred while the MV MASFIVE 6 barge was returning to Malaysia from the Philippines.
Many Western and other embassies routinely issue warnings against travelling to most of the Philippines' Muslim-populated southern regions, which lie just northeast of Sabah, because of the risk of being abducted by the Abu Sayyaf.
On Tuesday, officials said that 10 Indonesian sailors had been kidnapped in waters off the southern Philippines. The incident was believed to have happened last Saturday.
The Philippine military said initial information indicated the sailors may have been taken by an Abu Sayyaf faction to Sulu, a remote southern island that is a hideout of the militant outfit.
Someone claiming to be from Abu Sayyaf called the vessel's owners to demand a ransom for the sailors' release.
Other recent kidnappings, including of two Canadian tourists and a Norwegian resort owner in areas previously considered beyond the group's reach, have further raised fears.
Last year, Malaysian Bernard Then was kidnapped from a seaside restaurant in Sabah, about 300 kilometres (180 miles) from the Abu Sayyaf's Jolo stronghold. He was later killed by the group.
The Abu Sayyaf has staged cross-border raids into Malaysia before, including in April 2000 when gunmen seized 21 European and Asian tourists from a dive resort. They were released in batches after a ransom was paid the following year.
Founded in the 1990s with the help of late Al-Qaeda mastermind Osama Bin Laden, the Abu Sayyaf has been blamed for some of the Philippines' worst terror attacks, including bombings and kidnappings for ransom.