Taiwan is also demanding compensation and the arrest of those responsible.
It has warned the Philippines of diplomatic and economic measures if it does not respond positively.
The Philippine coastguard acknowledged that it had fired at the boat to "disable" its machinery.
It says that it was acting in self-defence.
Demands
Fisherman Hung Shih-cheng, 65, was shot dead on Thursday 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 exclusive economic zone.
Hours after his remains and vessel were returned to Taiwan, the president's office and the foreign ministry issued a series of demands to the Philippines.
They asked for a formal apology, the speeding up of the investigation into his death, punishment of the perpetrators, the payment of compensation to the fisherman's family and talks over fishing rights in the disputed area.
Taiwan also threatened to send the Philippines' representative back to Manila if its neighbour does not respond within 72-hours.
The BBC's Cindy Sui in Taiwan says that while the Philippines' representative to Taiwan has expressed sympathy and condolences to the victim's family, the Philippines has refused to apologise, pending the investigation.
Officials in Manila have said that their initial findings suggest that the coast guard acted in self-defence and that fishing boat tried to ram into the coastguard vessel.
The three surviving fishermen on board the vessel, including Mr Hung's son and son-in-law, have disputed this account.
After inspecting the boat, Taiwanese officials also said they did not find this explanation credible as there were 52 bullet holes in the boat and the fishermen were unarmed.
"This is very brutal and cold-blooded," Taiwanese President Ma Ying-jeou said on Saturday, warning that his country would consider sanctions against the Philippines amid widespread public anger towards Manila over the shooting.
Taiwanese officials say that the coastguard chased the boat for some time and did not offer help to the distressed vessel after it was damaged by the shooting.
It argues that opening fire on an unarmed fishing boat violated international law.
Tens of thousands of Filipino migrant labourers work in Taiwan's manufacturing sectors and homes.-British Broadcasting Corporation
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