Philippine representative Amadeo Perez said after returning to Manila from Taipei late Thursday that his government has verified at least one attack, in which a Filipino was beaten with a bat.
"He was brought to a hospital and police are investigating. We are documenting the cases," he said.
Taiwan has frozen the hiring of Filipino workers, cut trade exchanges and discouraged travel to the Philippines because of the fisherman's death. Its government brushed aside an apology from the Philippine president as insufficient.
Taipei is demanding compensation, investigation, punishment and negotiations on a fishing agreement. Perez said that there additional demands, which he did not specify before reporting to Philippine President Benigno Aquino III.
"At this time, Taiwanese people are emotional and tension is high," Perez said. "We advised Filipinos there not to leave home as much as possible. Eat your meals at home, and just commute directly between home and work for now."
Nearly 87,000 Filipinos work in Taiwan, a fraction of the roughly 10 million who work abroad to escape poverty and unemployment at home.
Perez said he may recommend the repatriation of Filipinos if the need arises. "We will not abandon our people," he added.
The Taiwanese government has asked Taiwanese to behave correctly with Filipinos.
Filipino workers in Taiwan who were interviewed by Manila radio stations complained that some shops refused to sell them goods and restaurants would not serve them. They did not give their names for fear of reprisals. A Taiwanese company that employs Filipinos printed a memo advising them to avoid fishing villages.
The circumstances behind the May 9 shooting of the fishermen remain in dispute, though the Philippines acknowledges that its coast guard personnel opened fire on a Taiwanese boat. Manila says the action was taken in self-defence to prevent the Taiwanese from ramming the coast guard vessel, but Taiwanese fishermen deny the ramming claim.
Both countries are investigating the incident. Fourteen Taiwanese police investigators are in Manila, and Philippine investigators will ask Taiwanese authorities for permission to inspect the fishing boat and interview the crew.
The hiring freeze has brought anxiety to Filipinos waiting to take up jobs in Taiwan.
"We are appealing. We hope there will be a solution to this because we are just trying to work for our family," said Zette Monleon, a factory worker who could not leave on her return trip to Taiwan because she was asked for additional documents, which could take weeks.
Trade between the Philippines and Taiwan is about $11 billion, with a surplus of $6.7 billion in Taiwan's favour.