Tokyo and Manila announced last week they would start formal talks "to delimit the maritime boundary" of an economic zone and continental shelf between them.
The announcement came as Philippine President Ferdinand Marcos met Japanese Prime Minister Sanae Takaichi on a visit to Tokyo.
Taiwan's sovereign rights over its territory and surrounding waters "are indisputable", Taipei's foreign ministry said in a statement.
"Given that the area that Japan and the Philippines plan to delimit through negotiations substantially overlaps with Taiwan's exclusive economic zone in waters east of Taiwan, Taiwan again calls on both countries to take this fact into full consideration, fully take Taiwan's rights and interests into account, and engage in consultations with Taiwan on relevant issues," the ministry said.
China, which claims Taiwan is part of its territory, has called the talks "illegal" and has also claimed exclusive control over the waters concerned.
Taipei rejects Beijing's claims, insisting Taiwan and China are "not subordinate" to each other.
Manila and Tokyo's shared grievances over Chinese maritime territorial claims have seen them draw increasingly close in recent years.
Like most countries, Japan and the Philippines do not recognise Taiwan's claim to statehood but maintain close unofficial relations.