However, Dmitry Peskov repeated Russia’s position that it would “not hand anyone over”.
Edward Snowden, 30, has been stuck in transit at a Moscow airport for the past month as he has no valid travel documents.
The US Attorney General, Eric Holder, has sought to assure Moscow he would not face the death penalty in America.
Washington wants him extradited for leaking details of surveillance programmes.
Dmitry Peskov did not specify what the nature of the talks between the agencies was.
He did, however, remind reporters that President Vladimir Putin had expressed a strong determination not to allow the case to interfere with US-Russian relations.
Vladimir Putin had not taken part in any discussions with the American authorities over Mr Snowden case, Dmitry Peskov said.
Edward Snowden “has not made any request that would require examination by the head of state”, Dmitry Peskov added.
The Russian president has refused to hand him to the American authorities, but said he could stay in Russia only if he stopped leaking US secrets.
Edward Snowden, whose passport has been cancelled by the US, has been in the transit area of Moscow’s Sheremetyevo airport since arriving from Hong Kong on June 23.
On Thursday Edward Snowden’s lawyer Anatoly Kucherena denied earlier reports that Snowden had been given Russian travel documents.
Edward Snowden has requested temporary asylum in Russia, and said recently his favored final destination was Latin America.
In a letter to Russian Justice Minister Alexander Konovalov, Eric Holder said that the charges against Edward Snowden were not punishable by death.
If additional charges were brought which could incur capital punishment, the US would not seek to impose such a penalty, he added.
The Snowden affair has caused diplomatic ructions around the world, upsetting America’s close allies and traditional enemies.
Leaks by the former CIA worker have led to revelations that the National Security Agency (NSA) is collecting Americans’ phone records.
On Wednesday evening, an attempt to block funding for the programme narrowly failed in a 205-217 vote in the House of Representatives.
The White House had lobbied Congress to support the surveillance.
Opponents of the US, including Bolivia, Venezuela and Nicaragua, have all offered Edward Snowden asylum.
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