Russia yesterday ordered the expulsion of the alleged US agent, identified as Ryan C Fogle, the third secretary of the political section of the US Embassy after airing footage of his capture while wearing a blonde wig.
McFaul arrived at the ministry for the 10:00 am local time (1130 IST) meeting but declined to speak to journalists at the entrance, Russian television reported. He was seen leaving the building after a brief meeting shortly afterwards.
The ministry had summoned McFaul for an explanation after slamming Washington for what it described as "provocative acts in the spirit of the Cold War".
Washington acknowledged the incident late yesterday.
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US State Department spokesman Patrick Ventrell confirmed that an American staffer at the embassy had been briefly detained, but refused to respond to allegations that the man was an undercover CIA agent.
Russian Foreign Minister Sergei Lavrov told journalists that he had opted not to bring up the case at yesterday talks with US Secretary of State John Kerry, however.
Footage published by state English language television RT showed Fogle being pinned face down to the ground and having his hands put behind his back for the arrest, while apparently wearing a blonde wig under his baseball cap.
He was then shown being questioned at the Federal Security Service (FSB) while documents such as his passport and a stack of 500 euro notes along with some letters were displayed.