The US has accused Russia of giving fugitive US intelligence leaker Edward Snowden a "propaganda platform".
President Barack Obama called Vladimir Putin after Mr Snowden met human rights groups at a Moscow airport - his first appearance since fleeing there from Hong Kong three weeks ago.
Mr Snowden has been charged with leaking classified US information.
He says he is seeking asylum in Russia to be able to travel to Latin America where he has been offered refuge.
But no request from Mr Snowden had arrived yet, the head of the Federal Migration Service, Konstantin Romodanovsky said on Saturday, according to Russian news agency Interfax.
The former CIA contractor has been stuck in the transit area of Sheremetyevo airport - reportedly staying at the airport's Capsule Hotel - since arriving from Hong Kong on 23 June.'Stop harming partners'
Details of the phone conversation between the two presidents were not immediately available, but the White House confirmed the Snowden case would be discussed.
"Providing a propaganda platform for Mr Snowden runs counter to the Russian government's previous declarations of Russia's neutrality," said White House spokesman Jay Carney ahead of the call.
"It's also incompatible with Russian assurances that they do not want Mr Snowden to further damage US interests."
The Kremlin's position is that the fugitive can stay in Russia as long as he stops leaking secrets about US surveillance schemes.
"Mr Snowden could hypothetically stay in Russia if he first, completely stops the activities harming our American partners and US-Russian relations and, second, if he asks for this himself," said President Putin's spokesman Dmitry Peskov.
The American has sent requests for political asylum to at least 21 countries, most of which have turned down his request. However, Bolivia, Nicaragua and Venezuela have indicated they could take him in.
But he is unable to leave the transit zone without asylum documents, a valid passport or a Russian visa - he reportedly has none of these documents.
And some European countries are likely to close their airspace to any plane suspected of carrying the fugitive.'Outside the law'
On Friday, Mr Snowden said in a statement he formally accepted all offers of support or asylum he had already received "and all others that may be offered in the future".
But he added that the US and some European countries had "demonstrated a willingness to act outside the law".
The status of asylum as well as criticism of alleged US spying on Latin American governments were on the agenda as members of the South American trade bloc, Mercosur, gathered in Uruguay.
The plane of Bolivian President Evo Morales, returning to Bolivia from Moscow, was last week forced to land in Austria after France, Portugal, Italy and Spain barred it from their airspace - apparently because of suspicions that Mr Snowden was on board.
Mr Snowden's leaking of thousands of classified US intelligence documents have led to revelations that the National Security Agency is systematically seizing vast amounts of phone and web data.
They have also indicated that both the UK and French intelligence agencies allegedly run similarly vast data collection operations, and the US has been eavesdropping on official EU communications.