Taiwan's leader on Friday called for calm and promised to protect Filipinos on the island amid widespread anger at the Philippines over the killing of a Taiwanese fisherman.
Anti-Manila sentiments mounted after a 65-year-old fisherman was shot dead last week by Philippine coastguards who said his vessel intruded into Philippine waters.
Taiwanese media have reported an attack on a Filipino, tourists cancelling planned visits to the Philippines and some supermarkets removing food from the Philippines from their shelves.
"We will continue negotiating the issue with the Philippines and I hope everyone can calmly and peacefully resolve the issue to avoid hurting bilateral ties," Ma said while meeting a group of international scholars.
Ma said he has instructed relevant Taiwanese units to protect some 87,000 Filipinos living and working on the island to ensure they are not harmed.
Taiwan's ETTV cable news channel reported that a Filipino was allegedly attacked by four Taiwanese wielding iron bars as he went to work in southern Taiwan. He was treated at hospital for a facial injury.
Taiwan's Foreign Minister David Lin also urged calm at a press conference aimed at seeking more international support for the diplomatically isolated island in the lingering dispute.
"We consider the Filipino people as our friends... We call on our people to treat them well, and our government will continue to provide a friendly environment for them," he said.
Only 23 countries have diplomatic relations with Taiwan. The Philippines officially recognises Beijing over Taipei but maintains trade ties with the island.
Taiwan has rejected Manila's claims that the incident took place in Philippine waters and that it was "unintended", while President Ma described the incident as "cold-blooded murder".
"If (Philippine) civil servants used automatic weapons to fire at unarmed and unprovocative fishing boats, this was not carrying out their job duties. This is cold-blooded murder," Ma said.
Taiwan has recalled its envoy, banned the hiring of new Philippine workers and staged a military drill in waters off the northern Philippines earlier this week.
A personal envoy for Philippine President Benigno Aquino was forced to return home on Thursday after Taipei rejected an apology he conveyed for the president.
Taipei has repeatedly pressed Manila to issue a formal government apology, to compensate the fisherman's family, and to apprehend the killer.