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"In accordance with established procedure, today we have sent a package of documents to the World Anti-Doping Agency. The package contains a notice about disagreement with Wada sanctions," Rusada director general Yury Ganus told reporters in Moscow.
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 Wada 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.
"The risks are considerable," he told reporters.
"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.
Speaking to AFP on Thursday, Ganus said his American and British counterparts could call for severe sanctions against Russia.
"There is such a possibility," he said.
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.
The significant extent of state-sponsored doping in Russia, notably between 2011 and 2015, was revealed in an independent report by sports lawyer Richard McLaren, released in 2016.
The issue has dealt a colossal blow to the status of post-Soviet Russia as a major sports power after hosting events such as the 2013 World Athletics Championships, the 2014 Winter Olympics in Sochi and the 2018 World Cup.
The Sochi Games later became notorious for the number of doping violations by prominent Russian athletes.
The doping scandal has also divided Russian sports stars, with three-time world champion high jumper Mariya Lasitskene calling for sports officials to be held to account over the ban.
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