Speaking after the announcement on the outcome of the RPC's appeal on Tuesday, Mutko called the CAS decision unlawful and politically motivated.
"There were no reasons to dismiss [the appeal] but it happened," Mutko was quoted as saying by the TASS news agency before adding "those bodies that should defend Paralympians do not do it and punish them instead".
Russia can now appeal to the Swiss Federal Court although it can only overturn the CAS ruling on the basis of a procedural mistake and not on the merits of the case.
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Alexei Karpenko, a lawyer representing the RPC, said an appeal would be considered once CAS had issued its full, reasoned decision.
Although not widely followed or celebrated in Russia, where rights campaigners say many disabled people are marginalised by regressive social attitudes and inadequate state support, Russian para-athletes are some of the best in the world.
Their team topped the medal table at the 2014 Winter Paralympics in the Russian city of Sochi after taking second place behind China at London 2012.
The country's exclusion from Rio will hit hard in a country that has long drawn pride and prestige from its history of sporting success.
Russia at the Sochi 2014 Paralympic winter games
Image credit: Reuters
Following Tuesday's verdict, the IPC said Russia had been banned for its inability to fulfil its membership "responsibilities and obligations", particularly the anti-doping code.
"Although we are pleased with the decision, it is not a day for celebration and we have enormous sympathy for the Russian athletes who will now miss out on the Rio 2016 Paralympic Games," said IPC president Philip Craven in a statement.
"It is a sad day for the Paralympic Movement but we hope also a new beginning," he said, adding that he wanted the ruling to be a "catalyst for change" in Russia.
The IPC said the 267 places secured by Russian athletes would now be redistributed.
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