Indonesia angrily summoned the ambassador of China to a meeting on Monday after the Chinese Coast Guard forcibly recovered a fishing boat confiscated by the Indonesian authorities, in a sign of escalating tensions between the two countries over the South China Sea.

The maritime confrontation also indicated that Indonesia might be toughening its stance toward China in the region.

The high-seas episode began at 10 p.m. on Saturday, when a special task force vessel operated by the Indonesian Ministry of Maritime Affairs and Fisheries caught a Chinese fishing boat within Indonesia’s maritime 200-mile exclusive economic zone, off the Natuna Islands northeast of Borneo, said Arrmanatha Nasir, a spokesman for Indonesia’s Foreign Ministry.

Indonesian personnel boarded the Chinese boat, the Kway Fey, took its captain and eight-member crew into custody, and began towing the ship back to a base in the Natuna Islands, he said.

But around midnight, he said, a Chinese Coast Guard vessel, which had been following the Indonesian ship, approached it, on or inside the 12-nautical-mile line marking Indonesia’s territorial waters.

“To prevent anything else occurring, the Indonesian authorities let go of the Chinese boat and then left toward Natuna, still with eight fishermen and the captain on board,” Mr. Arrmanatha said, adding that the Indonesian crew was “only lightly armed.”

Indonesia’s maritime and fisheries minister, Susi Pudjiastuti, held a news conference on Sunday and labeled the Chinese Coast Guard’s intervention “arrogant.”

On Monday morning, Retno Marsudi , the Indonesian foreign minister, met with Sun Weide, minister counselor of China’s Embassy in Jakarta, the capital, and handed over an official letter of protest about the confrontation.

Mr. Sun represented the embassy because the ambassador, Xie Feng, was out of the country.

Later on Monday, a spokeswoman for the Chinese Foreign Ministry, Hua Chunying, called the area where the episode took place “traditional Chinese fishing grounds” and said that the Coast Guard vessel had not entered Indonesian territorial waters.

“China immediately requested Indonesia to release the detained Chinese fishermen and ensure their physical safety,” she said at a regularly scheduled news conference in Beijing.

The confrontation was not the first between Indonesian and China over Chinese fishing vessels near the Natuna Islands, but the government in Jakarta has de-emphasized previous ones or kept them under wraps.

China is one of Indonesia’s largest trading partners and an important market for its commodities, including palm oil and coal. The countries recently signed an agreement for China to build a high-speed rail link between Jakarta and Bandung, the capital of West Java Province.

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In March 2013, an Indonesian Maritime Ministry vessel caught a Chinese fishing boat operating in the same region near the Natuna Islands and confiscated the vessel and detained its nine-person crew. Several hours later, the Indonesian ship was confronted by a Chinese vessel, reportedly armed with mounted machine guns and light cannons, which demanded the release of the boat and its crew.

Indonesia’s strong reaction to the latest confrontation, in particular because it may have occurred within its territorial waters, may have been a tipping point in how it deals with Chinese aggressiveness in the South China Sea, said Ian J. Storey, a senior fellow at the Institute of Southeast Asian Studies in Singapore, where he researches South China Sea disputes.

“I think we can say that it is far more serious than the 2013 incident, and I think the Indonesians will be apoplectic,” he said. “Indonesia has tended to downplay them, but they couldn’t this time, and it demonstrates how frustrated that people are getting with China.”

The episode occurred as multiple strains are growing in the region, where China has territorial disputes with four members of the 10-nation Association of Southeast Asian Nations, known as Asean.

Members of the group have increasingly expressed concern about China’s aggressive posture in the South China Sea, including naval standoffs and land reclamation projects in disputed areas, and the stationing of military personnel and surface-to-air missiles in the Paracel Islands.

Last week, Malaysia’s defense minister, Hishammuddin Hussein, raised the possibility of a “pushback” against China by Southeast Asian nations.

Indonesia is not a claimant in the disputes, but China’s contentious nine-dash line map, which marks its territorial claims to around 90 percent of the maritime region, appears to overlap with part of Indonesia’s maritime 200-mile exclusive economic zone around the Natuna Islands, according to analysts.

In November, however, China’s Foreign Ministry acknowledged Indonesia’s sovereignty over the Natuna Islands, although it did not address the issue of the exclusive economic zone.

Indonesia has said that China’s territorial claims in the South China Sea have no legal basis under international law. That assertion was made most recently by President Joko Widodo during a visit to Japan in March 2015, less than five months after he took office.

One of Mr. Joko’s main foreign policy goals is to transform Indonesia, an archipelagic nation of 250 million people, into a regional maritime power. The Maritime Ministry has initiated a policy of scuttling all ships confiscated for illegal activities, in particular fishing with Indonesia’s maritime economic zone.

Mr. Arrmanatha said the Chinese Coast Guard might have acted as it did on Saturday because it did not want the Indonesian authorities to confiscate and destroy the vessel.

Indonesia has been building its military presence in the Natuna Islands, according to analysts, and has contemplated deploying eight Apache attack helicopters it bought from the United States.

THE NEW YORK TIMES