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Russia is moving to take over an important natural gas joint venture, putting the investments of Shell and two Japanese energy trading companies at risk in a seizure of a significant foreign investment.

A decree issued by President Vladimir V. Putin on Thursday is directed towards Sakhalin-2, a project in Russia’s Far East that is a key exporter of liquefied natural gas to Japan. The Kremlin’s move raised concerns in Japan about the future of those shipments.

Gazprom, Russia’s natural gas monopoly, has a controlling 50 percent stake in Sakhalin-2, followed by Shell, the European oil giant, with 27.5 percent, and Mitsui and Mitsubishi, two energy firms based in Japan with shares totaling 22.5 percent.

The decree says that a new company will take over Sakhalin-2 and that the three foreign investors have one month to ask the Russian government to keep their stake in the new enterprise.

Shell has previously said it plans to exit the venture as part of its efforts to pull out of Russia because of the invasion of Ukraine.

On Friday, Shell said it was “assessing” the implications of Russia’s move but declined to comment further. Shell has already written off $1.6 billion of the value of Sakhalin-2.

mr. Putin’s move is the first time he has grabbed an international petroleum project since the invasion of Ukraine in February. During his two decades in power, though, the Russian government has played hardball with foreign oil and gas companies. Essentially, Mr. Putin and the Russian oil industry have wanted Western companies to bring to the table capital and technology but with Russian entities retaining control.

Shell led the way in developing Sakhalin-2, which is based on Sakhalin Island in the Pacific and was Russia’s first liquefied natural gas facility, sending its first cargo to Japan in 2009. It gave the country a foothold in the fast-growing fuel, which is chilled to a liquid so it can be transported on ships.

Building the project was tricky because the location was remote and rugged and the gas needed to be piped from icy waters off the northern coast of the island to a liquefaction and export terminal in the warmer sea to the south.

credit…Pool photo by Alexander Zemlianichenko

Shell originally had a majority stake but came under fire from the Russian authorities, mostly because of allegations of environmental violations. In 2007, Shell and its Japanese partners yielded to pressure to sell a controlling stake to Gazprom.

mr. Putin may be trying to avoid what has happened with another project on the island, Sakhalin-1. The facility has been operated by Exxon Mobil, which has a sizable minority stake and, like Shell, has also said it is pulling out of Russia. In recent months, oil exports from the facility have dropped sharply. In June, not a single tanker took crude oil from the facility compared to a prior average of about one ship every three days, said Viktor Katona, an analyst at Kpler, a firm that tracks petroleum shipping.

The presidential order is unlikely to inflict much immediate damage on Shell, Europe’s largest energy company, which reported a record $9.1 billion profit for the first quarter of this year, because of high oil and gas prices. It could, though, herald other strong-arm tactics against Western oil companies that still have assets in Russia.

After the invasion of Ukraine in February, Shell said it would exit Sakhalin-2 and other ventures in Russia, although it did not set a precise date or indicate what it would do with its stake and other ventures. In May, Shell sold its gasoline stations in Russia to Lukoil, a private Russian company.

If it gave up Sakhalin-2, Shell would also lose its share of the liquefied natural gas exported by the project, which amounted to about 5 percent of the company’s global LNG trading last year, according to an estimate by Bernstein, a research firm.

LNG may be a significant business for Shell, but Alexander McColl, an analyst at Bernstein, said the loss of Sakhalin 2 was “not a game changer” for Shell.

The smooth flow of fuel supplies from Sakhalin-2 to Japan and other countries may be the primary concern after this move. The facility may continue to function under its new ownership, but not having a leading LNG operator like Shell to work with Gazprom will not help in the long run, Mr. McCall said.

Both Mitsui and Mitsubishi said there had been no impact on production at Sakhalin-2 so far.

Sakhalin-2 has great importance to Japan, providing about 8 percent of the country’s liquefied natural gas, a mainstay of the power industry in recent years that was already under pressure.

After the Fukushima nuclear meltdown in 2011, Japan embraced liquefied natural gas as a fuel that was cleaner than coal and safer than nuclear. About one-third of Japan’s electricity now comes from power plants burning LNG In recent months, though, prices have soared as Japanese buyers found themselves in competition with utilities in Europe scrambling to make up for shortfalls of gas from Russia.

After Western oil companies announced plans to leave Russia after the invasion of Ukraine, Prime Minister Fumio Kishida said Japan could not afford to pull out of Sakhalin-2, which he described as “extremely important to Japan’s energy security.”

After mr. Putin’s move to take over the company, though, Mr. Kishida said the government needed to keep “a watchful eye on the kind of demands” the new arrangement may bring.

Ben Dooley and Hisako Ueno contributed reporting.

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