"We have said repeatedly that there can be no discussion of any official involvement of any Russian office, including the FSB, being involved in any unlawful cyber activities," said Kremlin (IOB: 0Q8D.IL - news) spokesman Dmitry Peskov.
He told reporters Russia had received no official word about the charges and was getting all its information from the media.
Around 500 million Yahoo users had their information accessed in the attack, which began in 2014, but continued until late last year.
In one of the biggest hacking operations ever, cyber criminals targeted security, diplomatic, military personnel and journalists, for espionage and financial gain.
One of the FSB agents charged was Dmitry Dokuchaev , an officer in the FSB's Centre for Information Security, the office tasked with investigating cyber crimes.
Dokuchaev is the FBI's point of contact for hacking in Moscow, which, according to acting assistant attorney general Mary McCord, made the offence "even more egregious."
He and his boss, Igor Suschin, are accused of running the Yahoo operation by hiring accused hackers Karim Baratov and Alexsey Belan, who has been on the FBI's most wanted list for three years.
:: Yahoo cyberattack trial would shine a light on Russian hacking
US authorities and cyber security specialists have been saying for years that the Kremlin employs criminal hackers, allowing the Russian government to advance its agenda while denying involvement.
Experts admit the US also uses hackers, sometimes to help find other cyber criminals, but Washington is far more cautious than it used to be about alerting Moscow to their presence.
Former FBI cyber agent Milan Patel, explained: "Magically those guys would disappear off the battlefield and most likely end up working for the Russian government."