The foreign ministry issued an official protest to the US ambassador who it summoned to an early morning meeting, but signs also grew that neither side wanted the Cold War-style incident to develop into a full scale crisis.
The suspected agent was caught red-handed late Monday as he tried to recruit a Russian security agent with an advance of USD 100,000 for intelligence on the Northern Caucasus, according to the Russian FSB security service.
"To say the least, we are surprised by the extremely crude and clumsy recruitment" that came after pledges by both sides to improve cooperation, said President Vladimir Putin's foreign policy advisor Yuri Ushakov, quoted by ITAR-TASS.
Ushakov also expressed surprise that it appeared vows by Putin and President Barack Obama for special services to work closer together had not filtered through to the CIA or the US embassy.
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He said: "I do not think that what has happened will influence this cooperation, all the more as its importance has been agreed at a high level."
The suspected agent, named as Ryan C Fogle, was handed back to the US embassy and ordered to leave the country after being declared persona non grata.
The Kommersant daily said that Fogle was likely to have been seeking intelligence about the Boston marathon bombers whose origins were in the Russian Northern Caucasus, despite pledges by security services to cooperate in the investigation.
The foreign ministry said that Deputy Foreign Minister Sergei Ryabkov had issued a formal protest to US ambassador to Moscow Michael McFaul.
In Washington, State Department acting deputy spokesman Patrick Ventrell confirmed McFaul had met with Ryabkov, but refused to go into the details of a "private diplomatic conversation".
Ventrell would also not divulge whether the US embassy official had now left Russia, saying only "we do comply with our Vienna Convention obligations and requirements when countries ask us to send someone home".