Because the treaty proscribes testing ground-launched cruise missiles of medium-range, the Kremlin cannot undo the violation. But administration officials do not believe the cruise missile has been deployed and say there are measures the Russians can take to ameliorate the problem.

Image President Vladimir V. Putin of Russia on Sunday aboard a ship in Severomorsk, Russia. Credit... Pool photo by Mikhail Klimentyev

Administration officials declined to say what such steps might be, but arms control experts say they could include a promise not to deploy the system and inspections to demonstrate that the cruise missiles and their launchers have been destroyed. Because the missiles are small and easily concealed, obtaining complete confidence that the weapons have been eliminated might be difficult.

NATO’s top commander, Gen. Philip M. Breedlove, has said that the violation requires a response if it cannot be resolved.

“A weapon capability that violates the I.N.F., that is introduced into the greater European land mass, is absolutely a tool that will have to be dealt with,” he said in an interview in April. “It can’t go unanswered.” Mr. Obama has determined that the United States will not retaliate against the Russians by violating the treaty and deploying its own prohibited medium-range system, officials said. So the responses might include deploying sea- and air-launched cruise missiles, which would be allowable under the accord.

Republican lawmakers have repeatedly criticized the administration for dragging its feet on the issue. Ms. Gottemoeller, the State Department official, has had no discussions with her Russian counterparts on the subject since February. And Mr. Kerry’s call on Sunday was the first time he had directly raised the violation with Mr. Lavrov, State Department officials said. Administration officials said the upheaval in Ukraine pushed the issue to the back burner and that the downturn in American-Russian relations has led to an interruption of regular arms-control meetings.

The prospects for resolving the violation were also uncertain at best. After Ms. Gottemoeller first raised the matter in 2013, Russian officials said that they had looked into the matter and consider the issue to be closed.

The Russians have also raised their own allegations, a move that American officials believe is intended to muddy the issue and perhaps give them leverage in any negotiations over compliance. One month after Ms. Gottemoeller raised the American concerns, the Russians responded by pointing to the United States plans to base the Aegis missile system in Romania.