Barack Obama has called on Russian president Vladimir Putin to pull his forces back to their bases in Ukraine's Crimean region and not to interfere elsewhere in the former Soviet republic.
The US president personally delivered the message to Mr Putin during a 90-minute telephone conversation, the White House said.
But his request is likely to go unheeded as the Kremlin said Mr Putin, in turn, emphasised to Mr Obama the existence of real threats to the life and health of Russian citizens living in Ukraine and that Russia has the right to protect its interests there.
Russian troops took over Crimea as the Russian parliament gave Mr Putin a green light yesterday to use the military to protect its interests in Ukraine.
Ukraine's newly-installed government was powerless to react to the swarm of Russian troops.
"President Obama expressed his deep concern over Russia's clear violation of Ukrainian sovereignty and territorial integrity," the White House said in a statement that called the action "a breach of international law".
Hours earlier, Mr Obama's national security team huddled at the White House to get updates on the situation and discuss policy options. Mr Obama did not participate but vice president Joe Biden and secretary of state John Kerry took part by video conference.
"The United States condemns Russia's military intervention into Ukrainian territory," the White House said.
Mr Obama also discussed the situation with French president Francois Hollande and Canadian prime minister Stephen Harper, whose country has withdrawn its ambassador from Moscow.
US defence secretary Chuck Hagel spoke by telephone to his Russian counterpart and stressed that "without a change on the ground" Russia risked further instability in the region, isolation in the international community and an escalation that would threaten European and international security, the Pentagon said.
Mr Kerry said he spoke to Ukraine's president Oleksandr Turchynov "to assure him he had the strong support of the United States" and also convened a call with his counterparts from around the world to co-ordinate their next steps.
But a defiant-sounding statement issued by the Kremlin in Moscow said Mr Putin stressed to Mr Obama that the situation in Ukraine posed "real threats" to Russian citizens and compatriots who live in Ukrainian territory.
"Vladimir Putin emphasised that, in the case of a further spread in violence in eastern regions (of Ukraine) and Crimea, Russia maintains the right to protect its interests and the Russian-speaking population that lives there," the Kremlin said.
Mr Obama told Mr Putin that the appropriate way for him to address concerns about the treatment of ethnic Russian and minority populations in Ukraine was to do so peacefully through direct contact with Ukraine's new government and through international observers. He said the US was prepared to help mediate such a dialogue.
Mr Obama also made clear that Russia's continued violation of Ukraine's sovereignty and territorial integrity would have a negative effect on Russia's standing in the world.
He said on Friday that "there will be costs" to Russia for military intervention in Ukraine. But he and the European allies he has pledged to consult with regularly on this issue have limited options.
Mr Putin has so far dismissed the few specific threats from the United States. The US and Europe are not obligated to come to Ukraine's defence because it does not have full-member status in Nato, while broader international action through the United Nations seems all but impossible because of Russia's veto power as a permanent member of the Security Council.
Administration officials said on Friday that Mr Obama might retaliate by cancelling a trip to Russia in June to attend the Group of Eight international economic summit and could also cut off trade talks with Moscow.
The White House said yesterday that the US would suspend upcoming participation in "preparatory meetings" for the summit, which is being planned for the Black Sea resort of Sochi, the site of the just-completed Winter Olympics.
Political turmoil in Ukraine pushed President Viktor Yanukovych from office following massive pro-democracy protests after he rejected a partnership agreement with the European Union in favour of deepening his country's historical ties with Moscow.
Mr Yanukovych held a news conference in southern Russia on Friday in which he said he was not asking Moscow for military assistance and called such action "unacceptable". Mr Yanukovych, who still considers himself Ukraine's president, also vowed to "keep fighting for the future of Ukraine" and blamed the US and the West for encouraging the rebellion that forced him to flee last weekend.
The EU agreement Mr Yanukovych rejected would have paved the way for Ukraine's greater integration with the West, including potential affiliation with Nato. Russia strongly objects to Nato membership for former Warsaw Pact members and Soviet republics.
Associated Press journalists on Ukraine's Crimean Peninsula saw a convoy of hundreds of Russian troops heading toward the regional capital, Simferopol.
On the road from Sevastopol, the Crimean port where Russia maintains a naval base, to Simferopol this morning, journalists saw 12 military trucks carrying troops, a Tiger vehicle armed with a machine gun and also two ambulances.