"The two leaders noted the importance of U.S.-Russian bilateral relations and discussed a range of security and bilateral issues, including the status of Mr. Edward Snowden and cooperation on counter-terrorism in the lead-up to the Sochi Winter Olympics," the White House said Friday following the phone call.
Kremlin spokesman Dmitry Peskov said Obama initiated the call, RIA Novosti reported.
Snowden has taken up residence in the transit zone of Sheremetyevo International Airport in Moscow, after fleeing Hong Kong June 23 to escape U.S. prosecution for his release of secret information about U.S. surveillance programs.
Putin has said Snowden can stay in Russia only if he stopped releasing U.S. secrets.
In a meeting with members of human rights organizations at the airport Friday, Snowden said he planned to ask Russia for temporary asylum while he arranged safe passage to Latin American countries that have offered him refuge.
White House press secretary Jay Carney told reporters Friday the United States does not believe the Snowden situation "should, and we don't want it to do harm to our important relationship with Russia."
"And we continue to discuss with Russia our strongly held view that there is absolute legal justification for him to be expelled, for him to be returned to the United States to face the charges that have been brought against him for the unauthorized leaking of classified information," Carney said.
However, he said Snowden's appearance at the airport Friday was "incompatible with Russian assurances that they do not want Mr. Snowden to further damage U.S. interests."
"And I would simply say that providing a propaganda platform for Mr. Snowden runs counter to the Russian government's previous declarations of Russia's neutrality and that they have no control over his presence in the airport," he said.
In a statement Friday, Jamil Dakwar, human rights director of the American Civil Liberties Union, accused the United States of having "improperly interfered" with Snowden's asylum rights.