NATUNA ISLANDS, Indonesia — Dedi knows where the fish run strongest in Indonesian waters off the Natuna islands. The Chinese know, too.

Backed by armed Chinese Coast Guard ships, Chinese fishing fleets have been raiding the rich waters of the South China Sea that are internationally recognized as exclusively Indonesia’s to fish.

While Mr. Dedi catches the traditional way, with nets and lines, the steel Chinese trawlers scrape the bottom of the sea, destroying other marine life. So not only does the Chinese trawling breach maritime borders, it also leaves a lifeless seascape in its wake.

“They come into our waters and kill everything,” said Mr. Dedi, who like many Indonesians goes by a single name. “I don’t understand why our government doesn’t protect us.”

Wary of offending Indonesia’s largest trading partner, Indonesian officials have played down incursions by Chinese fishing boats, trying to avoid conflict with Beijing over China’s sprawling claims in these waters. But with the Chinese presence growing more aggressive, fishers in the Natunas are feeling vulnerable.

“There was a vacant period, then China came back,” said Ngesti Yuni Suprapti, the deputy regent of the Natuna archipelago. “Our fishermen feel scared.”

The latest episode occurred in February, fishers said, when Chinese fishing boats flanked by Chinese Coast Guard vessels dropped their trawl nets yet again. It seemed as if the coronavirus outbreak peaking in China at the time hadn’t diminished the country’s global ambitions.

The Indonesian fisheries ministry, however, denied any intrusion by the Chinese. The Indonesian government does not provide data on incursions by foreign fishing boats.

China’s illegal fishing near the Natunas carries global consequence, reminding regional governments of Beijing’s expanding claims to a waterway through which one-third of the world’s maritime trade flows. But local leaders in the Natunas don’t control what happens near their shores.

“We only have authority over our land,” said Andes Putra, the head of the Natunas’ Parliament. “The provincial and central governments handle the seas.”

Yet with multiple agencies responsible for protecting the seas — the navy, the coast guard, the marine police and the fisheries ministry, to name a few — decision-making is diffuse, analysts said.

“There is a lack of a single coherent lead agency or a single coherent policy for maritime security,” said Evan Laksmana, a senior researcher at the Center for Strategic and International Studies in Jakarta, the Indonesian capital. “The Chinese can take advantage of that.”

Chinese impunity was on full display in January when President Joko Widodo of Indonesia visited the Natunas.

“There is no bargaining when it comes to our sovereignty,” Mr. Joko said. Earlier, Indonesian fighter jets buzzed the sky, while warships patrolled the seas.

But the day after Mr. Joko left the Natunas, the Chinese showed up again. Its fishing fleet, backed by the Chinese Coast Guard, took days to leave the area, local officials and fishers said.

The fisheries ministry denied that any such incident had taken place.

On Chinese maps, a line made of nine dashes scoops out most of the South China Sea as China’s. One of the dashes slices through waters north of the Natunas.

While Beijing recognizes Indonesian sovereignty over the Natunas themselves, the Chinese Foreign Ministry describes the nearby sea as China’s “traditional fishing grounds.”

“Whether the Indonesian side accepts it or not, nothing will change the objective fact that China has rights and interests over the relevant waters,” Geng Shuang, a Chinese Foreign Ministry spokesman, said in January.

In 2016, an international tribunal dismissed the nine-dash line as legally baseless. The Chinese government ignored the ruling.

Instead, Beijing continued turning contested atolls and islets into military bases from which China can project its power across the South China Sea.

“Little by little, I think the Chinese will take the Indonesian sea, the Philippine Sea, the Vietnamese sea,” said Wandarman, a fisherman in the Natunas. “They are hungry: oil, natural gas and lots and lots of fish.”

The Chinese fishers are helping feed the country’s growing appetite for seafood by trawling the South China Sea.

But they are also serving a broader purpose.

“Beijing wants Chinese fishers to operate here,” said Ryan Martinson, an assistant professor at the China Maritime Studies Institute at the United States Naval War College, “because their presence helps to embody China’s maritime claims.”

During Mr. Joko’s first term, his fisheries minister, Susi Pudjiastuti, stood up to China and other countries illegally operating in Indonesian waters.

The navy fired warning shots at Chinese fishing boats. Ms. Susi ordered the seizure of foreign boats. She had dozens blown up.

One, a Vietnamese trawler, still slumps half submerged in a Natuna harbor.

As a result of Ms. Susi’s boat-sinking policy, the Chinese boats stopped intruding in large numbers, fishers in the Natunas said.

“She protected us, and she protected Indonesia,” said Idil Basri, the captain of a Natuna fishing boat.

But Ms. Susi’s stance, while popular with the public, irked others in government, who found her too confrontational, political analysts said. When Mr. Joko chose his ministers for his second term last October, Ms. Susi, a fishing magnate, was gone, replaced by a minister considered more conciliatory to China.

In the Natunas, the change was almost immediate, fishers said.

“The Chinese boats came back,” Mr. Dedi said.

In late October, one day after Mr. Joko’s new cabinet was installed, Mr. Dedi’s boat was well within the 200-nautical-mile exclusive economic zone in which only Indonesians are permitted by international law to fish.

A Chinese Coast Guard vessel appeared, then another. Mr. Dedi scrambled to record video of his boat’s coordinates, 72 nautical miles north of the Natunas.

While it is not illegal for foreign military vessels to transit through these waters, the coast guard ships were protecting Chinese trawlers.

After handing over his video to local maritime authorities, Mr. Dedi waited for action. Nothing happened, so he posted it on Facebook. Indonesian security services called him, he said, and sounded vaguely threatening.

Mr. Dedi continued to have run-ins with Chinese boats through February. In one case, he was in a standoff with the Chinese for an hour before he turned around for lack of Indonesian backup.

“We left, but they were still there in Indonesian waters,” Mr. Dedi said.

China’s buildup on disputed outposts in the South China Sea has boosted the ability of its coast guard to ply the waters near the Natunas. During storms, Chinese fishing boats can shelter at these artificial islands, too.

In 2016, as Indonesian authorities tried to tow in a Chinese boat operating off the Natunas, a Chinese Coast Guard ship nosed in and broke the towline, allowing the Chinese fishers to flee.

To counter China’s presence, Indonesia began building a military base in the Natunas four years ago. Today, the facility is moldering, empty of all but a few soldiers.

Jakarta’s latest tactic is to relocate hundreds of fishers from the populous Indonesian island of Java to the Natunas to act as maritime sentries.

But fishers in the Natunas oppose the idea, since the Javanese are subsidized by the state and do the same destructive bottom trawling as the Chinese.

Mr. Wandarman said that because of the profusion of foreign boats in recent months, his catch had declined by half.

But fishing is his livelihood, Mr. Wandarman said. The island he lives on has only two traffic lights, and not much to support it economically besides the sea.

“Our boats are small and wooden, and the Chinese Coast Guard is armed and modern,” Mr. Wandarman said. “My fear out there is bigger than the sea is big.”

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