China condemned Taiwanese authorities on Wednesday after two Chinese nationals died in a boat accident while pursued by Taiwan's coast guard.

The Chinese boat was carrying four people when it capsized near the Kinmen Islands, throwing all onboard into the water, Chinese and Taiwanese authorities said.

"The malignant incident severely harmed the feelings of compatriots on both sides of the Taiwan Straits," Zhu Fenglian, a spokesperson for China's Taiwan Affairs Office, said in a statement.

Taiwan's coast guard said the speedboat had "illegally (entered) Taiwanese waters", the island's CNA news agency reported.

The coast guard "immediately requested that the boat submit to an inspection, but it resisted and capsized as it sped away," CNA said.

Beijing has urged the Taiwanese authorities to immediately investigate the incident, Zhu added.

CNA said all four were rescued from the water and sent to hospital.

"Two were pronounced dead after efforts to resuscitate them failed," the coast guard said.

"The other two are in stable condition and have been brought to Kinmen for further investigation by prosecutors," it added.

The Kinmen Islands are controlled by Taiwan but lie within sight of China's coast.

China claims democratic Taiwan as its own, although it has no sovereignty over the territory of 23 million people and its adjacent islands.

The incident comes against a backdrop of high tensions across the Taiwan Strait.

Taiwan's presidential election, held in January, was won by the ruling Democratic Progressive Party's Lai Ching-te, who Beijing regards as a "separatist". 

Chinese President Xi Jinping has ceaselessly called for the reunification of Taiwan with China, more than 70 years since the two split at the end of a civil war in 1949.