The Philippines on Tuesday agreed to apologize for the fatal shooting last week of a fisherman from Taiwan by Filipino coast guard officers.

The agreement was announced hours before an ultimatum from Taiwan for an apology was due to expire at midnight.

Demonstrators protest near the Philippine consulate in Hong Kong on Tuesday. A Taiwan fisherman was killed by the Philippine Coast Guard on Thursday. TYRONE SIU / REUTERS

Manila agreed to apologize, clarify the truth, punish those held responsible and start early negotiations with Taiwan on a fishery agreement.

But it has not officially agreed to pay compensation for the incident, in which coast guards killed a 65-year-old fisherman on Thursday, Taiwan media reported.

Reports said the Philippines will send Amadeo Perez, chairman and chief executive officer of the Manila Economic and Cultural Office, as an envoy to Taiwan on Wednesday to make a promise on compensation and to visit the victim's family.

Observers said the deal, in which Manila acknowledges its mistakes, can largely satisfy Taiwan's demands and ease public outrage on the island.

On Saturday, Taipei issued a 72-hour ultimatum to the Philippines to make an official apology, or face sanctions including a freeze on sending Filipino workers to the island.

There are about 87,000 Filipino domestic helpers and other workers in Taiwan, who send home hundreds of millions of dollars a year.

Taiwan also sent four coast guard and naval vessels to protect its fishermen in waters near the Philippines at the weekend.

It is unclear whether Taiwan will still conduct a naval drill in the waters where Hung Shih-cheng, skipper of the 15-metric-ton Guang Ta Hsin 28 was shot dead. Taiwan authorities said earlier on Tuesday the decision would depend on the reaction of the Philippine government.

Yang Baoyun, an expert on Southeast Asian studies at Peking University, said the possibility of Taipei staging the exercise still exists, but the scale and intensity might be reduced.

"Under the new circumstances, the military exercise could take the form of routine maritime patrols to account for heightened public sentiment, to better protect fishermen and to further deter the Philippine side," Yang said.

Beijing on Tuesday voiced support for Taiwan, saying it has always firmly safeguarded Taiwan compatriots' security and legitimate rights, Xinhua News Agency reported.

"We hope the Philippines will conduct a thorough investigation into the incident and provide a concrete explanation at an early date," Foreign Ministry spokesman Hong Lei said at a regular news conference.

On Friday, the Philippine Coast Guard admitted the shooting, which left more than 50 bullet holes in the fishing vessel, but insisted it happened within its own waters.

This claim was denied by the victim's son, who was with his father and two other fishermen on the boat at the time, as well as by Taiwan authorities who said the incident happened in an overlapping area of the two sides' exclusive economic zones.

Luo Yuan, deputy secretary-general of the China Military Science Society of the Chinese People's Liberation Army, said the Philippines brutally violated international law.

On Monday, Washington urged all sides "to refrain from provocative actions", while Philippine President Benigno Aquino called for calm, and guaranteed an in-depth investigation into the incident.

On Sunday, Antonio Basilio, resident representative of the Manila Economic and Cultural Office in Taiwan, visited the victim‘s family, and "extended condolences and apologies".

But Taiwan was not satisfied with these actions. Hundreds of fishermen burned Philippine flags, and hurled eggs at the Manila Economic and Cultural Office in Taipei on Monday.

Li Guoqiang, deputy director of the Center for Chinese Borderland History and Geography at the Chinese Academy of Social Sciences, said Manila's response came late, as it was stuck in an "awkward situation".

"The Philippines believed the incident area was within its own territory, so answering Taipei's requests means a retreat from its previous territorial claims; but Manila cannot stay silent as well."

Li also said Manila had tried to play down the incident but strong reactions from Beijing and Taipei made this attempt difficult.