A report by The Philippine Star newspaper cited an unnamed official close to the Philippine government's investigation as saying coast guard personnel appeared to be on the defensive and they may have violated rules.
That is what the investigation has shown so far," said the official during an interview with the Star.
"While it could have been self-defense, the next questions would be was it proper to immediately fire the shots," he said. "What are the rules of engagement? Given that they acted in self-defense, is it justifiable to fire right away?"
The National Bureau of Investigation is expected to report this week on the incident May 9 that soured relations with Taiwan.
Politicians in both countries have called for the public to remain calm amid rising tensions in which the Philippines has issued a formal apology, which was rejected by Taiwan.
The incident happened May 9 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 and shot at the engine and propeller of the fishing boat to disable it, 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.
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 death prompted strong reactions from the highest levels of Taiwan's government including stern statements by Taiwanese Premier Jiang Yi-huah.
He said his government "is assessing the matter" after rejecting two apologies delivered by Philippines diplomats.
Jiang reiterated earlier Taiwanese demands for compensation for the victim's family and that the Philippines investigates the shooting and punishes those responsible.
Last week Taiwan threatened to cut flight connections with the Philippines but immediately imposed other 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.
A spokeswoman for Philippines President Benigno Aquino said the government wouldn't speculate on what the NBI report might say in its report this week.
"We will not respond. We don't want to escalate things any further," deputy presidential spokeswoman Abigail Valte said.
She also rejected allegations by a team of Taiwanese investigators in the Philippines that the coast guard crew fired with intent to harm the crew of the Taiwanese boat, The Philippines Star reported.
Amadeo Perez Jr., chairman of the Manila Economic and Cultural Office -- who as an emissary of Aquino to delivered an apology to Taiwan last week -- blamed Taiwanese media waging a hate campaign against the Philippines.
"We advised Filipinos there not to leave home as much as possible," he said. "Eat your meals at home and just commute directly between home and work for now.''
The Taiwanese government stopped short of withdrawing work visas for the 88,000 Filipino migrants working in Taiwan.
But Taiwan's Council of Labor Affairs won't process any of the usual 3,000 applications for work permits it receives from Filipinos each month, a report by CNA said.
Taiwan also halted business promotion activities, bilateral agricultural and fishery cooperation have been stopped. The government suspended high-level exchanges, including ministerial-level meetings at this week's World Health Assembly in Switzerland.