Deputy presidential spokesman Manolo Quezon said the Philippines “has to do its part to enforce the sanctions”.
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.
What impact will sanctions have?
Will carrots or sticks change North Korea?
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”.Ocean Maritime Management was blacklisted by the UN Security Council in 2014 after one of its ships was seized in July 2013 near the Panama Canal with Cuban weapons hidden under sugar sacks.
It was accused last year of renaming and reflagging its vessels to evade asset freezes.
The Jin Teng was sailing under a Sierra Leone flag.
Pyongyang reacted to Wednesday’s sanctions by firing six short-range missiles into the sea.
Leader Kim Jong-Un later ordered that the country’s nuclear weapons should be “ready for use” at any time.
North Korea sanctions explained
Jump media player
Media player help
Out of media player. Press enter to return or tab to continue.
Media captionJohn Sudworth reports from Dangdon in China on the continuing trade between North Korea and China
What exactly is banned?
The export of coal, iron and iron ore used for North Korea’s nuclear or ballistic missile programmes.
All gold, titanium ore, vanadium ore, rare earth minerals and aviation fuel exports.
Any item (except food and medicine) that could develop North Korea’s armed forces.
Small arms and light weapons are now included in an arms embargo.
Upmarket watches, watercraft, snowmobiles and other recreational sports equipment added to a ban on luxury goods.
No vessels or planes can be leased or registered to North Korea.
What are the other measures?
Member states must inspect all cargo to and from North Korea, not just those suspected of containing prohibited items.
An asset freeze on North Korean funds linked to nuclear and missile programmes.
Foreign financial institutions cannot open new offices in North Korea without approval, and North Korean banks cannot open offices abroad.