More than 1,000 American military personnel will leave Niger in the coming months, Biden administration officials said on Friday, upending U.S. counterterrorism and security policy in the tumultuous Sahel region of Africa.

In the second of two meetings this week in Washington, Deputy Secretary of State Kurt M. Campbell told Niger’s prime minister, Ali Lamine Zeine, that the United States disagreed with the country’s turn toward Russia for security and Iran for a possible deal on its uranium reserves, and the failure of Niger’s military government to map out a path to return to democracy, according to a senior State Department official, who spoke on the condition of anonymity to discuss diplomatic talks.

The decision was not a particular surprise. Niger said last month that it was revoking its military cooperation deal with the United States following a highly contentious set of meetings in Niger’s capital, Niamey, with a high-level American diplomatic and military delegation.

That move was in keeping with a recent pattern by countries in the Sahel region, an arid area south of the Sahara, of breaking ties with Western countries. Increasingly, they are partnering with Russia instead.

American diplomats have sought in the past several weeks to salvage a revamped military cooperation deal with Niger’s military government, U.S. officials said, but in the end they failed to strike a compromise.

The talks collapsed amid a growing wave of ill feelings toward the U.S. presence in Niger. Thousands of protesters in the capital last Saturday called for the withdrawal of American armed forces personnel only days after Russia delivered its own set of military equipment and instructors to the country’s military.

Niger’s rejection of military ties with the United States follows the withdrawal of troops from France, the former colonial power that for the past decade has led foreign counterterrorism efforts against jihadist groups in West Africa, but which has lately been perceived as a pariah in the region.

American officials said on Friday that discussions with Niger to plan out an “orderly and responsible withdrawal” of forces would begin in the coming days and that the process would take months to complete.

Many of the Americans posted to Niger are stationed at U.S. Air Base 201, a six-year-old, $110 million installation in the country’s desert north. But since the military coup that ousted President Mohamed Bazoum and installed the junta last July, the troops there have been inactive, with most of their MQ-9 Reaper drones grounded except those flying surveillance missions to protect the U.S. troops.

It is unclear what access, if any, the United States will have to the base in the future, and whether Russian advisers and perhaps even Russian air forces will move in if Niger’s relations with the Kremlin deepen.

Because of the coup, the United States had to suspend security operations and development aid to Niger. Mr. Bazoum is still under arrest, eight months after he was ousted. Nevertheless, the United States had wanted to maintain its partnership with the country.

But the sudden arrival of 100 Russian instructors and an air-defense system in Niger this past week made the chances of cooperation in the short term even more unlikely. According to Russia’s state-owned news outlet Ria Novosti, the Russian personnel are part of Africa Corps, the new paramilitary structure intended to take the place of the Wagner group, the military company whose mercenaries and operations spread in Africa under the leadership of Yevgeny V. Prigozhin, who was killed in a plane crash last year.

The demonstrators in Niamey on Saturday waved Russian flags as well as those of Burkina Faso and Mali, two neighboring countries where military-led governments have also called in Russian assistance to help fight insurgents affiliated with the Islamic State and Al Qaeda.

American officials say they have tried for months to prevent a formal rupture in relations with Niger’s junta.

The new U.S. ambassador to Niger, Kathleen FitzGibbon, one of Washington’s top Africa specialists, has held regular discussions with the junta since officially taking office at the beginning of the year.

In a trip to Niger in December, Molly Phee, an assistant secretary of state for African Affairs, said the United States intended to resume security and development cooperation with Niger, even as she called for a swift transition to civilian rule and the release of Mr. Bazoum.

But the Pentagon has been planning for the worst-case contingencies if the talks failed. The Defense Department has been discussing establishing new drone bases with several coastal West African countries as backups to the base in Niger, which is landlocked. Talks are still in the early stages, military officials said, speaking on the condition of anonymity to discuss operational matters.

Current and former security and diplomatic officials said Niger’s strategically significant location and willingness to partner with Washington will be difficult to replace.

J. Peter Pham, a former special U.S. envoy to the Sahel, said in an email, “While the ordinary people of Niger will bear the brunt of the consequences of an American military withdrawal and the subsequent loss of political and diplomatic attention, the United States and its allies also lose, at least in the short term, a strategic military asset that will be very difficult to replace.”