The 6,830-tonne cargo ship Jin Teng will not be allowed to leave Subic port, northeast of the capital Manila, where it had been docked for three days and its crew will be deported, presidential spokesman Manolo Quezon said on state-run radio station Radyo ng Bayan.
It was the first reported enforcement of the sanctions, the toughest to date, which were adopted late Wednesday by the UN Security Council.
"The world is concerned over North Korea's nuclear weapons programme and as a member of the UN, the Philippines has to do its part to enforce the sanctions," Quezon said.
A team from the UN is expected to inspect the ship in the port, located near a former United States naval base, foreign affairs spokesman Charles Jose said.
Jose told AFP the ship was impounded "in compliance with the UN resolution" regardless of the results of the inspections.
The Jin Teng, carrying palm kernels, was searched for the second time on Saturday, this time using electronic weapons sensors, coastguard spokesman Commander Armand Balilo told AFP, adding the 21 crewmen were "very cooperative".
Balilo said no explosives, drugs or banned substances have been found so far.
- AFP