Justice Secretary Leila de Lima confirmed a report by the Philippine Daily Inquirer that the ministry's National Bureau of Investigation had recommended criminal charges be filed.
De Lima also said she had submitted the NBI report to President Benigno Aquino this week, the Inquirer reported.
The investigation surrounded the May 9 death of fisherman Hung Shih-chen on the Taiwanese fishing boat Guan Ta Hsin 28 in the Balintang Channel. The incident sparked a diplomatic row between Manila and Taipei.
The killing in waters both countries claim is another incident highlighting disputed maritime boundaries and fishing rights in the highly contentious South China Sea.
The incident happened between the northern tip of the Philippines and the southern coast of Taiwan. A Philippines coast guard surveillance vessel encountered four Taiwanese fishing boats in waters the Philippines considers an exclusive economic zone, the Philippines coast guard said in a statement at the time.
The coast guard said one of the Taiwanese boats allegedly tried to ram the coast guard vessel as officers attempted to board the fishing boats. The coast guard fired warning shots, trying to disable the vessel, the statement said.
A crew member from one of the Taiwanese boats said the Philippines vessel shot at a fuel tank, resulting in the death of the 65-year-old fisherman.
De Lima said she couldn't confirm whether the NBI report also recommended employees of the Bureau of Fisheries and Aquatic Resources be prosecuted.
The BFAR owns the patrol vessel involved in the incident and which had two BFAR employees and 17 coast guard operatives on board.
The NBI is looking to have Hung's daughter, who brought murder charges against the coast guard, become a private complainant in the case should the president approve the recommended criminal charges, de Lima said.
She said the NBI report is "exhaustive" and based on "objective evaluation of evidence" made after careful deliberations. "As to whether [the findings are] acceptable, it remains to be seen," de Lima said.
She said Taiwan's separate investigation into the incident didn't influence the NBI investigation.
NBI investigators said they consulted their Taiwanese counterparts to discuss results of tests, share notes and evidence and exchange opinions, de Lima said.
The Inquirer report said coast guard spokesman Cmdr. Armand Balilo described the NBI report as "not final" and "not official."
The coast guard maintains its personnel fired in self-defense to deter the Taiwanese fishing boat from ramming their vessel.
Soon after the incident, both governments urged their citizens living in the other country to keep a low profile in public for their own physical safety.
Despite apologies from Philippines government envoys -- which Taiwan didn't accept -- and promises of a thorough investigation into the incident, Taiwan imposed retaliatory measures.
These included a controversial freeze of the importation of Filipino laborers and suspension of economic exchanges, a report by Taiwan's Central News Agency said at the time.