"We don't confirm" this information, foreign ministry spokeswoman Marzieh Afkham said when asked about the claim.
The US official, who spoke on condition of anonymity, had said the missiles crashed in Iran on Wednesday, but did not provide details about where they might have come down or whether they caused any damage, AFP reports.
Russia's defence ministry has denied the claim.
"Any professional knows that during these operations we always fix the target before and after impact.
All our cruise missiles hit their target," said ministry spokesman General Igor Konashenkov.
Moscow began its military campaign against terrorists in Syria on September 30 upon a request from the Damascus government, shortly after the upper house of the Russian parliament gave President Vladimir Putin the mandate to use military force in Syria.
Kalibr cruise missiles launched by ships of the Russian Navy’s Caspian Flotilla strike facilities of the ISIL terrorist organization in Syria with precision of up to three meters, the Russian Defense Ministry said on Wednesday.
The missile launches were in support of a major ground offensive by the Syrian army on several fronts in the west of country.