"He [Whelan] was caught red-handed", Russian Foreign Minister Sergei Lavrov said Wednesday, according to Reuters.
The 48-year-old MI resident was in Moscow to attend a wedding.
He said USA media reports claiming that Mr Trump might have been a Russian agent reflected a dramatic plunge in standards of journalism.
Russian Federation is a long-time supporter of Syrian President Bashar Al-Assad.
According to Radio Free Europe, Kremlin foreign policy aide Yury Ushakov told reporters that the talks between Putin and Abe would not be easy.
The United States has rejected a Russian offer to save the 1987 Intermediate-range Nuclear Forces (INF) Treaty that keeps nuclear missiles out of Europe, setting the stage for Washington to withdraw from the pact next month.
The Kremlin's hopes for better relations with the US under Trump have been shattered by ongoing investigations into the allegations of collusion between Trump's campaign and Russian Federation.
Mr Trump said this week he never worked for Russian Federation.
He particularly scoffed at the charges leveled against Trump's former national security adviser, Michael Flynn, saying that he only talked to the Russian ambassador in a bid to protect US interests.More news: Trump's 'Wounded Knee' tweet over Warren sparks anger
European allies are anxious about the deployment of United States missiles in Europe, as happened in the 1980s while being caught up in nuclear competition between Moscow and Washington.
Paul Whelan, an American man accused of spying in Russian Federation, was caught "red-handed" in his hotel, according to the country's foreign minister.
Lavrov denied claims Whelan was arrested in order to conduct a prisoner swap with the U.S.
"These are not pre-conditions, it's just an effort to understand why Japan is the only country in the world which can not say: "I accept the results of World War Two in their entirety", Lavrov told a news conference.
"We weren't able to break any new ground yesterday with Russia", Thompson said of the January 15 meeting with Russian Foreign Ministry officials.
"He was caught red-handed", Foreign Minister Sergey Lavrov said on Wednesday.
Lavrov promised US diplomats can make a second visit to the detainee, and an Irish diplomat will also be visiting him soon.
Lavrov said the investigation into Mr Whelan continued and his detention was not motivated by any desire to try to exchange him for Russian citizens held in the US.