Two warships from the Japan Maritime Self-Defense Force (JMSDF) will take part in the exercise with a single Philippine ship after making a port call in the Philippines this month, said Vice Admiral Jesus Millan.
"This is a port call, a regular port call of the Japanese navy and while they are here, it would be good if we can practise this code of unplanned encounters at sea," he said.
The Japanese vessels would be leaving Subic while a Philippine ship was heading there under the training scenario, he said.
Millan said Japanese and Philippine sailors would have an opportunity to "compare notes" during the exercise, but stressed it had nothing to do with the Philippines' territorial dispute with China over conflicting claims to large parts of the sea.
The Philippines has been seeking closer ties with regional allies amid what it sees as Chinese aggression in pressing its territorial claims.
Millan said that practising with the Japanese force would help with modernising the poorly-equipped Philippine military, one of the weakest in the region.
China and Japan have their own festering territorial row over the East China Sea including ownership of the Senkaku islands, which Beijing also claims and calls the Diaoyus.
There have been regular standoffs in the sea and air around the contested territory.
Earlier this month, Japanese and Philippine coast guards held anti-piracy drills in the Philippines, the first such joint exercise between the two countries following a brutal occupation by Japanese forces during World War II.
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