Philippine investigators have recommended criminal charges be filed against coastguard personnel for the fatal shooting of a Taiwanese fisherman, the justice secretary said on Thursday.

"The NBI (National Bureau of Investigation) has recommended the filing of criminal and administrative charges against the Philippine coastguard personnel," Justice Secretary Leila de Lima told AFP in a text message from Madrid, where she is on an official trip.

De Lima said she could not disclose the specific charges pending clearance from President Benigno Aquino, whose office is reviewing the recommendation.

The May 9 incident occurred in waters near a Philippine island that Taiwan also claims as part of its economic zone.

A 65-year-old Taiwanese fishermen was killed when Philippine coastguard personnel opened fire on the small fishing vessel he was in.

The Philippines had initially insisted that the fishing boat intruded into its waters, and that coastguard personnel were forced to open fire when it tried to ram their vessel.

The coastguard also said immediately after the incident that it had nothing to apologise for.

But the killing caused widespread outrage in Taiwan, with the government in Taipei imposing economic sanctions on the Philippines and demanding an investigation, as well as a sincere apology.

A spokesman for Aquino said Thursday the president's office had received the report from the justice department about the incident.

But the spokesman, Ricky Carandang, would not comment further.

The defacto Taiwanese embassy in Manila, the Taiwan Economic and Cultural Office (TECO), had no immediate comment.

"We will wait until the final report of the Philippines (is) revealed. Only then will we have an official comment," David Chen, assistant to the TECO representative, told AFP.