"We don't confirm" this information, foreign ministry spokeswoman Afkham Marzieh 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.
Russia's defence ministry has flatly 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.
Russia posted a graphic on the defence ministry website Wednesday showing 26 missiles overflying Iran and Iraq before striking inside Syria, where it has been conducting air strikes in defence of President Bashar al-Assad since September 30.
The missile launches were in support of a major ground offensive by the Syrian army on several fronts in the war-torn country's west.