Angry Taiwanese fishermen burned Filipino flags in protest Monday after the Philippine coastguard fired on a Taiwan fishing boat killing a crew member.
Philippine President Benigno Aquino called for calm as tensions escalated between the two countries over last week's incident in which the 65-year-old fisherman was shot dead.
Hundreds of fishermen wearing yellow headbands and chanting "Justice must be done!" and "Killer must be punished!" hurled eggs at the Philippine de facto embassy in Taipei, which was guarded by dozens of police.
Aquino said Monday that the embassy in Taiwan was in talks with Taiwanese foreign ministry officials and had assured them an investigation was being carried out.
"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.
Taiwanese authorities said more than 50 bullets hit the 15-tonne vessel, and fisherman Hung Shih-cheng was killed.
The victim's son, who was with his father and two other sailors on the boat at the time, has insisted they did not cross into Philippine waters.
Prosecutor Liu Chia-kai described the incident as "nothing but a slaughter", after examining the boat after it was towed back from sea.
Taiwan's government has come under pressure from the opposition and the media to take action.
US State Department spokeswoman Jen Psaki told reporters Washington was urging all sides to "to refrain from provocative actions".
"The United States has been in touch with both the Philippine government and the Taiwan authorities regarding this incident. And we welcome the Philippine government's pledge to conduct a full and transparent investigation," she said.
Aquino declined to comment on demands by Taiwan at the weekend for his government to apologise for the shooting and pay compensation to the victim's family, or face a potential freeze in sending Filipino workers to the island.
There are about 87,000 Philippine domestic helpers and other workers in Taiwan, who send home hundreds of millions of dollars a year.
Taiwan at the weekend sent four coastguard and naval vessels to protect its fishermen in waters near the Philippines.
The Philippine government said on Sunday that Antonio Basilio, head of the Philippines' de facto embassy in Taiwan, had visited the family of the fisherman and "extended condolences and apologies".
Aquino said he did not want to comment further, preferring to let diplomats handle the dispute.
"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.