The M/V Jin Teng, a 6,830 deadweight tonne (dwt) cargo ship with its 21 North Korean crew, left on Thursday afternoon for China after clearing immigration, customs, quarantine and port authorities, said coastguard spokesman Commander Armand Balilo.
"At the policy level, there is no more basis to continue to hold M/V Jin Teng after U.N. Security Council delisted it from the annex of UNSC Resolution 2270," Charles Jose, a foreign ministry spokesman, said in a text message.
No team from the United Nations came to inspect the ship but local authorities did not find any contraband on board except some broken aids to navigation equipment, the coastguard said.
Tough new U.N. sanctions, passed in March to punish North Korea after its fourth nuclear test in January, blacklisted 31 ships owned by North Korean shipping firm Ocean Maritime Management Company (OMM). The sanctions aim to starve North Korea of money for its nuclear weapons programme.
But the U.N. Security Council agreed earlier this week to China's request to remove sanctions on four ships blacklisted for ties to Pyongyang's arms trade. China said the ships were not OMM ships and secured a commitment that the ships would no longer use North Korean crews.
The four ships included the Jin Teng, detained by the Philippines days after the sanctions took effect.
Jin Teng, flying a Sierra Leone flag, arrived in the Philippines on Feb. 27 and was unloading palm kernels when it was seized.
The Jin Teng has called at Palembang, Indonesia, and Kaohsiung, Taiwan, since the beginning of this year, ship tracking data available on the Reuters Eikon Terminal showed. (Reporting By Manuel Mogato; Editing by Michael Perry)