By Kanupriya Kapoor and Agustinus Beo Da Costa

JAKARTA (Reuters) - The Indonesian president will travel to the Natuna Islands for the first time on Thursday to assert Indonesia's sovereignty, a senior official said, after China said earlier this week it had an "overlapping claim" over nearby waters.

Beijing said on Monday that waters near the Natuna Islands were subject to overlapping claims on "maritime rights and interests" between China and Indonesia.

Indonesia's foreign minister on Wednesday rejected China's stance, saying the waters were in Indonesian territory.

"Our position is clear that claims can only be made on the basis of international law. For Indonesia, we don't have overlapping claims in any form in Indonesian waters with China," Indonesian Foreign Minister Retno Marsudi told reporters.

The chief security minister, foreign minister, and the heads of the individual military branches will accompany the president on his trip to Natuna, Cabinet Secretary Pramono Agung told reporters.

Asked the reason for the trip, he told reporters, "Natuna is the territory of Indonesia, that is final. As head of the government and the state, the president wants to ensure that Natuna is part of Indonesia's sovereignty."

The remote island chain has a small civilian population. Jakarta objects to Beijing's inclusion of waters around the islands within China's "nine-dash line", a demarcation line used by Beijing to show its claim to the South China Sea.

Despite the objection, Indonesia is not part of a broader regional dispute over China's reclamation activities in the South China Sea and Beijing's claims on swathes of key waterways.

China's Foreign Ministry said over the weekend that an Indonesian naval vessel fired on a Chinese fishing boat near the chain of islands on Friday, wounding one person.

Indonesia's navy responded that it had fired warning shots at several boats with Chinese flags it accused of fishing illegally but that nobody had been wounded.

It was the third reported confrontation near the Natuna Islands this year and comes amid rising regional tensions over China's assertiveness in the South China Sea.

Indonesian Vice President Jusuf Kalla told Reuters on Monday the Southeast Asian nation would be more assertive in protecting its exclusive right to the waters around the Natuna Islands.

Despite this more assertive stance, Retno said relations between the two countries remained good.

"This is a matter of law enforcement, not politics," she said.

(Addditional reporting by Jakarta bureau; Writing by Randy Fabi; Editing by Michael Perry and Raissa Kasolowsky)