Najib's comments came after the Philippine military said it was working to verify reports that Malaysian national Bernard Then had been beheaded by his captors, the Islamic militant group Abu Sayyaf.
"I, the government, and all Malaysians are shocked and sickened by the murder of our countryman Bernard Then, and we condemn it in its strongest terms," Najib said in a statement on his Facebook page.
"We call upon authorities to take action against those who have perpetrated this savage and barbaric act and ensure that they are brought to justice," said Najib, who is currently in Manila for an Asia-Pacific summit.
A woman who was abducted along with him, Thien Nyuk Fun, was released last week following negotiations between the captors and authorities on both sides.
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Founded in the 1990s with the help of Al-Qaeda mastermind Osama Bin Laden, the Abu Sayyaf has been blamed for some of the worst terror attacks in Philippine history, including bombings and kidnappings for ransom.
"The (military) and (police) headquarters have indeed received news about the inhuman, barbaric and brutal incident in the island of Jolo," Philippine military spokesman Colonel Restituto Padilla said in a statement, referring to Then's case.
Padilla denied there was any link to the Asia-Pacific Economic Cooperation (APEC) forum being held in Manila and attended by top world leaders including US President Barack Obama.
The killing is unusual for the Abu Sayyaf, which has usually preferred to hold their foreign captives for lengthy periods, sometimes years, in exchange for ransom money.