A criminal investigation into espionage has been launched against the U.S. citizen. The charges he faces could carry a prison term of as much as 20 years, according to Russia's criminal code.
American citizen Paul Whelan was arrested over three days ago in the Russian capital, the FSB was cited as saying by TASS news agency. "We have requested this access and expect Russian authorities to provide it", the department said.
The latest round of sanctions "in response to Russia's continued disregard for worldwide norms", which includes Moscow's suspected interference in the 2016 US election, were announced earlier this month.
It provided no further details.
The arrest comes during an extended period of tension in relations between Moscow and Washington, particularly over the issues of election hacking and influence peddling.
Russia detains US citizen suspected of spying
Earlier this month, Russian gun rights activist Maria Butina pleaded guilty to conspiring with a senior Russian official to infiltrate USA conservatives.
Russian officials denied Butina is one of their agents.
In the past, Russian Federation has arrested foreigners with the aim of trading prisoners with other countries.
The agency said the American was detained "while carrying out an act of espionage".
"I don't know whether a meeting will happen", Putin said during a press conference, according to CNN.
The United States is entangled in other prominent cases of detentions that appear to be arbitrary and retaliatory actions taken by authoritarian governments. Earlier this month, a third Canadian citizen was detained in China.
Relations between the White House and the Kremlin are fraught over accusations that Russian Federation meddled in the 2016 United States presidential election, sanctions against Moscow and disagreements over an arms control treaty.