Two Chinese fishers have drowned after their boat capsized during pursuit by Taiwan's coast guard off an island close to China but effectively controlled by Taiwan.

Taiwanese and Chinese authorities say the fishing boat capsized on Wednesday afternoon near Kinmen Island, which lies near the city of Xiamen in China's Fujian Province.

All four people on the Chinese boat were thrown into the sea, and two of them died.

Taiwan's Mainland Affairs Council said the Chinese boat was operating inside what Taiwan calls "prohibited waters" and that it capsized while trying to flee from the coast guard.

The council expressed deep regret over what it called an unfortunate incident resulting from the boat's refusal to cooperate with law enforcement. It said the coast guard had done nothing wrong and called on China to crack down on similar actions.

China's Taiwan Affairs Office spokesperson issued a statement condemning Taiwan's actions. The office called it a malicious incident that significantly hurt the emotions of compatriots on both sides of the strait.

It said Taiwan's ruling Democratic Progressive Party has made various excuses in the past to treat the mainland's fishers in a violent and dangerous manner.

Taiwan authorities had been stepping up patrols in waters near Kinmen Island after a series of sightings of what appeared to be Chinese fishing vessels.