The master and chief engineer have been abducted from a ro-ro off the Philippines.
Authorities have blamed Abu Sayyaf gunmen for the latest attack on shipping in the region.
Lt Commander Alvin Dagalea, station commander of the Philippine Coast Guard, identified the men as captain Aurelio Agacac and chief engineer Laurencio Tiro from the 17,900-gt Super Shuttle Roro 9 (built 1980), operated by Asian Marine Transport Corp.
It was boarded off Basilan on Thursday while en route to General Santos City, the Inquirer daily said.
Dagalea said the coast guard sent a gun boat to pursue the abductors, who were last reported to be heading for Tuburan town on three speedboats.
But the military has freed two Malaysian men kidnapped by Abu Sayyaf from a tug, Serudung 3.
