Chinese vessels have occasionally entered Indonesia-claimed areas of the North Natuna Sea at the southern edge of the South China Sea, drawing protests from Jakarta.
"The China Coast Guard ship re-entered the Indonesian jurisdiction in the North Natuna Sea on Wednesday," Indonesia's Maritime Security Agency said in a statement Thursday.
An Indonesian coast guard ship intercepted the boat and drove it from the area, it said.
The agency said the vessel first entered contested waters on Monday and when an Indonesian ship tried to contact the Chinese boat by radio, the Chinese coast guard said the area was part of Beijing's jurisdiction.
The ship was "disturbing the activity of a survey" being conducted by state-owned oil company Pertamina, it said.
An Indonesian coast guard ship shadowed the ship and drove it away.
Huge unexploited oil and gas deposits are believed to lie under the South China Sea's seabed, though estimates vary greatly.
The incidents are an early test for newly inaugurated President Prabowo Subianto who has pledged to bolster the defence of Indonesian territory.
In 2020 Indonesia deployed fighter jets and warships to patrol the Natuna islands waters in a spat with Beijing after Chinese vessels entered the area.
Beijing and Jakarta are key economic allies but the world's largest archipelago nation is trying to stop foreign vessels from fishing in its waters, saying it costs the economy billions of dollars annually.
China claims almost the entire South China Sea and has ignored an international tribunal ruling that its assertions have no legal basis.
It has deployed military and coast guard vessels in recent months in a bid to eject the Philippines from a trio of strategically important reefs and islands in the contested waterway.
It has also been ratcheting up pressure over a disputed island group controlled by Japan in the East China Sea, rattling Tokyo and its allies.
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