Aquino said Manila's de facto embassy in Taiwan was in talks with Taiwanese foreign ministry officials and had assured them an investigation was being carried out into last week's incident.
"I think it is in the interest of both parties to proceed in a calm basis," Aquino told reporters. "We are proceeding in that manner."
The Philippine coastguard admitted on Friday to firing at one of four Taiwanese fishing vessels that it said had strayed into the country's waters. A 65-year-old Taiwanese fisherman died in the confrontation.
There are about 87,000 Philippine domestic helpers and other workers in Taiwan who send home hundreds of millions of dollars a year.
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Taiwan also sent four coastguard and naval vessels on the weekend to protect its fishermen in waters near the Philippines.
The Philippine government said yesterday that Antonio Basilio, head of the Philippines' defacto embassy in Taiwan, had visited the family of the fisherman and "extended condolences and apologies".
"If we comment on that (at the presidential) level, we guarantee the issue will escalate," Aquino said.
The incident comes at a time of heightened tensions around the region over rival claims to the nearby South China Sea.
China, the Philippines, Taiwan, Vietnam, Malaysia and Brunei all have competing claims to parts of the sea.
Taiwan has ruled itself since 1949, but China still considers the island part of its territory. The Philippines, like most countries, officially recognises China over Taiwan but maintains trade ties with the island.