Philippine President Benigno Aquino has sent a representative to apologise for the death of a Taiwanese fisherman, his spokesman said, amid a deepening row.
The envoy would convey "deep regret and apology" over the incident, spokesman Edwin Lacierda said.
The move came hours after Taiwan suspended hiring Filipino workers and recalled its envoy from Manila.
Taiwan said the move showed President Ma Ying-jeou's "strong dissatisfaction" with Manila's handling of the case.
Taipei had earlier rejected an apology from the Philippines' top diplomat in Taipei.
The fisherman, Hung Shih-cheng, was shot by the Philippine coast guard last week in waters both sides claim.
'Lacked sincerity'
Mr Aquino had sent Manila Economic and Cultural Office Chairman Amadeo Perez as his personal representative to "convey his and the Filipino people's deep regret and apology" to the fisherman's family, Mr Lacierda the president's spokesperson said in a statement late on Wednesday afternoon.
There was no immediate response from Taipei. A Taiwan Foreign Ministry spokesperson had earlier suggested that the envoy was ""not sufficiently authorised" and would not be met, Taiwan's state-run news agency CNA reported.
Taiwan rejected an apology early on Wednesday from Antonio Basilio, head of the Philippine Representative Office in Taiwan.
Mr Basilio, whose apology came after a three-day deadline set by Taiwan expired, said that Manila had agreed to compensate the fisherman's family and conduct a joint investigation into the incident.
However, Taiwan's president felt the apology did not come from a high enough authority and lacked "sincerity", his spokeswoman said.
He suspended the processing of work visas for Filipinos and asked Mr Basilio to return to the Philippines to "help properly handle" the case.
Taiwan's Premier Jiang Yi-huah also told reporters that he was dissatisfied with the apology because it came from the representative office, not the Philippine government, and because the statement had been changed several times.
Taiwan instead demanded a "formal apology" from Manila, compensation for the victim's family, investigation and punishment for those responsible for the shooting, and the commencement of bilateral fishing talks.
It threatened more measures if such an apology was not forthcoming, including issuing a travel warning to discourage Taiwanese people from visiting the Philippines, stopping all high-level exchanges and carrying out a military exercise in the disputed waters.
'Honest living'
In Manila, Mr Lacierda said that government had "already started" an investigation, and was committed to a "thorough, exhaustive, impartial and expeditious investigation".
"We understand the grief and hurt of the family and of the people of Taiwan over this unfortunate loss and we empathise with them," he added in the statement.
He urged Taiwan not to involve Filipino workers in the country, saying that were "there working for an honest living".
There are about 88,000 Filipino migrant workers in Taiwan, most of whom work in the manufacturing sector, the BBC's Cindy Sui in Taipei reports.
Taiwan's labour office receives around 3,000 work applications from the Philippines each month, our correspondent adds.
Mr Hung, the 65-year-old fisherman, was shot dead on 9 May when the coastguard vessel opened fire on his boat.
He was in waters south-east of Taiwan and north of the Philippines, an area considered by both countries to be their 200 nautical mile-from-shore exclusive economic zone.
The Philippine coast guard said its crew believed he was trying to ram their vessel - claims the Taiwanese fishermen have denied.
Maritime tensions in the South China Sea have been heightened in recent months. China, Taiwan, the Philippines, Malaysia, Vietnam and Brunei have competing territorial claims in the region.
These disputes have existed for years but in recent months China has been taking a more assertive stance - prompting a robust response from some nations.
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