Ganus, who has long argued for a major crackdown by Russia against doping cheats, warned that the legal challenge could backfire, however.
The formal statement of disagreement with WADA will trigger an appeal process against the ban at the Lausanne-based Court of Arbitration for Sport (CAS).
Ganus, whose rigorous stance puts him at odds with his own government and supervisory board, argues that Moscow needs to accept the sanctions and own up to its faults in order to be able to reform. He however said he was obliged to relay the position of the supervisory board. He said he also sent a letter to WADA informing the anti-doping agency of his personal stance.
"I regret to inform you that all my attempts, including attempts to introduce changes to the RUSADA notice, have failed," said the letter.
Ganus told AFP on Thursday that "it is practically impossible" to contest the ban. WADA this month banned Russia for four years from major global events, including the 2020 Tokyo Olympics and the 2022 World Cup in Qatar, over manipulated doping data.
Under the sanctions, Russians will still be allowed to compete, but only as neutrals and if they can demonstrate that they were not part of what WADA believes was a state-sponsored system of doping.
Putin has called the sanctions politically motivated, indicating a lengthy legal battle loomed. He argued that the majority of Russian athletes were clean and should not be deprived of the right to compete under the Russian flag due to the actions of some individuals.
Ganus warned that contesting the doping ban could in fact make matters worse because CAS could make sanctions against Russia more severe. "We are creating a platform for it. We themselves are creating risks," he said.
"First of all, it would be a public hearing," he said, adding that some officials could request that the Court of Arbitration for Sport toughen up rather than soften the punishment against Russia. He referred to the position of United States Anti-Doping Agency chief Travis Tygart who has called for a blanket ban on Russian athletes at the Tokyo Olympics.
Tygart said that allowing "neutral" Russian athletes to compete at the Olympics in 2016 and 2018 had been ineffective. "WADA must get tougher and impose the full restriction on Russian athlete participation in the Olympics that the rules allow," Tygart said in November.
Speaking to AFP on Thursday, Ganus said he had information that his British counterpart could also call for severe sanctions against Russia. The suspension was handed to Russia over falsifying data from a doping testing laboratory that was handed to WADA earlier this year as part of a compliance re-instatement process.