Foreign ministry spokeswoman Maria Zakharova confirmed at a briefing in the capital that the 48-year-old would face trial, and dismissed suggestions he could be used in a prisoner swap for a Russian held in the US.
Mr Whelan – a former US marine born in Canada to British parents, and who now lives in Michigan – was taken into custody at the end of last month and could face 20 years in jail if convicted of spying.
His family said he was attending the wedding of fellow ex-serviceman, with his twin David Whelan, insisting that his innocence is “undoubted”.
Speaking during a visit to Singapore last week, British Foreign Secretary Jeremy Hunt warned the Kremlin not to use UK citizens in “diplomatic chess games”, with relations between the two countries having soured significantly since the poisoning of former spy Sergei Skripal and his daughter Yulia in Salisbury last March.
The same nerve agent used in the attack subsequently claimed the life of 44-year-old Dawn Sturgess.
Mr Hunt told Sky News that “individuals should not be used as pawns of diplomatic leverage”.
“We are giving him (Mr Whelan) every support that we can, but we don’t agree with individuals being used in diplomatic chess games,” he added.
“Because it is desperately worrying, not just for the individual but their families, and we are extremely worried about him and his family as we hear this news.”
Speculation that Russia may be holding Mr Whelan in the hope of securing a prisoner swap came after a former CIA chief based in Moscow said the Kremlin was keen to see the release of guns rights activist Maria Butina.
Daniel Hoffman suggested that Vladimir Putin had ordered the arrest of Mr Whelan to set up a trade for Butina, who last month pleaded guilty to acting as a Kremlin agent to infiltrate the National Rifle Association.
Moscow claims the 30-year-old was forced to make a false confession about being a Russian spy, after she admitted trying to collect intelligence on conservative political groups as Donald Trump rose to power.