Russian missile to test Trump administration.

WASHINGTON — Russia has secretly deployed a new cruise missile despite complaints from U.S. officials that it violates a landmark arms control treaty that helped seal the end of the Cold War, administration officials say.

The move presents a major challenge for President Donald Trump, who has vowed to improve relations with President Vladimir Putin of Russia and to pursue arms accords.

The new Russian missile deployment also comes as the Trump administration is struggling to fill key policy positions at the State Department and the Pentagon — and to settle on a permanent replacement for Michael Flynn, the national security adviser who resigned late Monday. Flynn stepped down after it was revealed that he had misled the vice president and other officials over conversations with Moscow’s ambassador to Washington.

The ground-launched cruise missile at the center of U.S. concerns is one that the Obama administration said in 2014 had been tested in violation of a 1987 treaty that bans U.S. and Russian intermediate-range missiles based on land.

The Obama administration had sought to persuade the Russians to correct the violation while the missile was still in the test phase. Instead, the Russians have moved ahead with the system, deploying a fully operational unit.

Administration officials said the Russians now have two battalions of the prohibited cruise missile. One is still located at Russia’s missile test site at Kapustin Yar in southern Russia near Volgograd. The other was shifted in December from that test site to an operational base elsewhere in the country, according to a senior official who did not provide further details.

It is very unlikely that the Senate, which is already skeptical of Putin’s intentions, would agree to ratify a new strategic arms control accord unless the alleged violation of the intermediate-range treaty is corrected. Trump has said the United States should “strengthen and expand its nuclear capability.” But at the same time, he has talked of reaching a new arms agreement with Moscow that would reduce arms “very substantially.”

The deployment of the system could also substantially increase the military threat to NATO nations, depending on where the highly mobile system is based and how many more batteries are deployed in the future.

Jim Mattis, the U.S. defense secretary, is scheduled to meet Wednesday with allied defense ministers in Brussels.