The Jin Teng is one of 31 ships operated by North Korean firm Ocean Maritime Management, which is subject to an asset freeze and sanctions.
It is currently docked in Subic Bay and is unloading palm kernels.
New UN sanctions were imposed after North Korea`s recent nuclear and ballistic missile tests.
They include mandatory inspections of all cargo going to or from the DPRK.
The Philippines government says it will impound the Jin Teng and eventually deport the crew.
Safety issues were reportedly found during an inspection of the vessel by the Philippine coast guard on Friday.
A second inspection took place on Saturday, coastguard spokesman Commander Armand Balilo told AFP news agency.
He said the crew of 21 had been "very cooperative".
More about:
-1780923278.jpg&h=190&w=280&zc=1&q=100)
