After the recent killings, Mr. Yanukovych reached a tentative truce with opposition leaders in talks brokered by the foreign ministers of France, Germany and Poland, but within 24 hours he fled Kiev, Ukraine’s capital, and an overwhelming majority of lawmakers voted to strip him of power, saying he had abandoned his position.

On Friday, a week later, Mr. Yanukovych resurfaced for a news conference in Rostov-on-Don, Russia, in which he said he was still the legitimate president and urged Russia not to intervene militarily in Crimea.

Mr. Obama’s warning suggested a deepening uncertainty among American officials about Mr. Putin’s intentions in the region despite a series of high-level contacts in recent days, including a telephone call between the two presidents one week ago. Mr. Yanukovych was an ally of Russia, and his toppling has left the Kremlin grappling for a response.

While American officials said that intelligence indicated that a Russian operation was underway, Mr. Obama stopped short of calling it an invasion. Part of the confusion, one official said, was that Russia routinely moves troops between military bases in Crimea.

Another American official said that intelligence reports from the region were “all over the place,” but that the administration believed that Russia had moved some of its forces into Ukraine, while some of the movement, officials said, seemed to be an increase in protective measures around Russian military installations.

Though he threatened an unspecified cost to Russia, Mr. Obama has limited options to respond to an intervention. Officials said he could cancel his participation in a Group of 8 meeting in Sochi, Russia, in June. The administration could also break off talks on a potential trade agreement. Russia sent a delegation to Washington this week to explore closer trade and commercial ties.