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"We have repeatedly explained that Russian government structures do not have any relationship with hacking," Deputy Foreign Minister Sergei Ryabkov said on Wednesday in comments carried by the Interfax news agency.
The Russian embassy in Qatar also shrugged off the claims, saying the Qatari authorities had not contacted the embassy about it.
CNN reported that US investigators assisting the Qatari government in their probe into the alleged hacking believe that Russia was behind the breach in May.
The stories included statements of support to Iran by the emir of Qatar, Tamim Bin Hamad Al Thani. Doha said the remarks were fabricated.
Iran is Saudi Arabia's regional rival, and the comments prompted angry reactions Riyadh and other Gulf capitals, culminating in the decision this week by six Arab states to break ties with Qatar.
"The official authorities of Qatar have not contacted the Russian embassy in Doha for information regarding the alleged hacking attack from the Russian side," the embassy said in comments carried by Russian state news agency TASS.
The Kremlin has been batting away hacking accusations for months.
On Tuesday, it denied allegations of Russian government hacking after revived claims in US media that Russia committed cyberattacks intended to influence last year's US presidential election in favour of Donald Trump, who had vowed to improve relations with Russia.
Last week Russian President Vladimir Putin rejected speculation that the Russian government has employed hackers to influence elections.
"Regarding hacking attacks in general, I tell you, this has, in a strange way, turned into a very fashionable, popular subject," Ryabkov said Wednesday.