Nine others were rescued by two passing ships in turbulent waters off Calayan island on Tuesday night, Vice Admiral Wilfredo Tamayo said.
"Those rescued were seen clinging to the half-submerged ship," Tamayo said, adding it was difficult to search for the others because of poor visibility and bad weather conditions.
"We were told rescuers in the area were encountering strong winds, huge waves and poor visibility," he added.
Rescue teams including vessels and aircraft had been sent to look for the missing crew and passengers.
The Mark Jason I left Manila a week ago with 14 crew and six other men bringing heavy equipment to Batanes island, off the northern tip of the main Luzon island.