It is the latest move by a Southeast Asian nation against Beijing's actions in the strategic waterway, which it claims almost in full.
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-5402 (CCG-5402) re-entered the Indonesian jurisdiction on Friday," Indonesia's Maritime Security Agency said in a statement Saturday.
The same ship first entered the disputed waters on Monday and again on Wednesday, with Indonesian patrol ships driving it away both times, the agency said.
It added that the Chinese vessel on Monday had disrupted a survey being conducted by state-owned oil company Pertamina, and that when contacted by an Indonesian ship, the Chinese coast guard said the area was part of Beijing's jurisdiction.
Indonesia said the area was recognised as its territory under international law.
"Indonesia has a sovereign right to explore the natural resource in that area and that cannot be disturbed by any country," the agency statement said.
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 has ignored an international tribunal ruling that its claims to almost all of the South China Sea 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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