JAKARTA--Indonesia said on Monday it had protested to Beijing over the presence of a Chinese coastguard vessel in its territorial waters near the disputed South China Sea, saying it marked a "violation of sovereignty."

The boat trespassed into Indonesia's exclusive economic zone off the coast of the northern islands of Natuna, Indonesia's foreign ministry said in a statement. It did not say when the incident occurred.

"The foreign affairs ministry has summoned the Chinese ambassador in Jakarta and conveyed a strong protest regarding this incident. A diplomatic note of protest has also been sent," it said.

The ambassador will report back to Beijing, but both sides have decided to maintain good bilateral relations, it said.

Local fishermen saw a Chinese coastguard vessel escorting fishing boats several times in recent days and then reported what they had seen to the Maritime Security Agency, media reports said.

Speaking in Beijing on Tuesday, Chinese Foreign Ministry spokesman Geng Shuang said China had sovereignty over the Spratly Islands and their waters and that both China and Indonesia have "normal" fishing activities there.

China's coastguard also carries out regular patrols there, he told a daily news briefing, without directly mentioning the Natuna Islands.

China's ambassador to Indonesia has already explained these points to the Indonesian government, Geng added.

Indonesia has no claims over the Spratly Islands, which lie to the northeast of the Natuna Islands.

Indonesia's foreign ministry reiterated its stance that the country is a non-claimant state in the South China Sea and that it has no overlapping jurisdiction with China.

However, Jakarta has clashed with Beijing before over fishing rights around the Natuna Islands and has also expanded its military presence in the area.

China claims most of the South China Sea, an important trade route which is believed to contain large quantities of oil and natural gas.

Beijing has been building artificial islands in the area, developments that have irked members of the Association of South East Asian Nations (ASEAN).

Brunei, Malaysia, Vietnam and the Philippines--all members of ASEAN--and also Taiwan also have claims in the sea.