The official cautioned there was so far no cause to suspect the abduction of the foreigners, who went missing late Monday along with a Malaysian off the state of Sabah on Borneo island.
The missing were identified as Spanish nationals David Hernandes Gasulla and Martha Miguel, and Hong Kong citizen Tommy Lam Wai Yin.
The Malaysian was identified only by one name, Ella.
"We believe they experienced an engine problem and could be drifting in their small fibre boat. The area they were travelling is quite safe," Mohamad Zubil Mat Som said.
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Two Malaysian warships, several smaller boats, and a helicopter were among the assets deployed in the operation, he added.
Islamic militants from the Abu Sayyaf group have been blamed for repeated kidnappings off Sabah of about 20 people.
Among the recent incidents, 10 Indonesian sailors were snatched from their tugboat in late March. They were released on Sunday.
Just over a week ago, however, Abu Sayyaf militants beheaded Canadian tourist John Ridsdel, for whom they had demanded USD 21 million in ransom.