Indonesia will summon China's ambassador over an incident involving a Chinese fishing vessel in the Natuna Sea, a minister said on Sunday, as Beijing accused it of attacking the ship in traditional Chinese fishing grounds.

The move comes amid heightened tensions in the South China Sea over China's land reclamation there and over its claims on vast swathes of an important shipping corridor. Several Southeast Asian countries have overlapping claims in the area.

Indonesia was attempting to detain the Chinese vessel for fishing illegally in waters near the contested South China Sea when a Chinese coast guard vessel intervened, fisheries minister Susi Pudjiastuti told reporters in Jakarta.

"What we will ask the ambassador is that if they say their nine-dash line does not claim Natuna then why is there still illegal fishing happening there," Pudjiastuti said, adding the ambassador will be summoned by the foreign ministry on Monday.

"Their government should not stand behind illegal and unregulated fishing," she said.

China's foreign ministry, in a statement sent to Reuters, said the trawler was carrying out "normal activities" in "traditional Chinese fishing grounds".

"On March 19, after the relevant trawler was attacked and harassed by an armed Indonesian ship, a Chinese Coast Guard ship went to assist," it said.

"The Chinese side immediately demanded the Indonesian side at once release the detained Chinese fishermen and ensure their personal safety," the ministry added.

China hopes Indonesia can "appropriately handle" the issue, it said. Indonesian foreign ministry officials were not immediately available for comment.

China claims vast swathes of the South China Sea that are also claimed by several Southeast Asian countries.

Indonesia is not a claimant in the disputed South China Sea, but has raised concerns over China's inclusion of the resource-rich Natuna Islands in its so-called "nine-dash line".

China says that it does not dispute Indonesia's sovereignty over the Natuna Islands.