Taiwan has recalled its representative to Japan over its handling of a ship collision in disputed waters earlier this week.

Japan contends the captain of a Taiwan leisure fishing boat is responsible for Tuesday's collision with a Japanese coastguard vessel near the Diaoyu Islands.

Taiwan's "foreign ministry" said on Saturday that the island "could not accept the Japanese conclusions of an investigative report" of the incident.

It has decided to recall its representative in Japan," it said.

The Taiwan captain, who was released on Friday, claims the Japanese vessel rammed his craft.

Japan said on Friday it wanted to avoid damaging relations after Taiwan protested against the holding of the captain. Two other crew members and 13 fishermen were released earlier.

Foreign ministry spokesman Qin Gang said on May 10 the Chinese government is dissatisfied with the actions of a Japanese Coast guard patrol boat.

"We are seriously concerned and strongly dissatisfied with the incident," Qin said at a regular press conference.