The ban was imposed last November by the International Association of Athletics Federations (IAAF) after an independent report uncovered rampant state-sponsored doping in Russian athletics.
The IAAF Council ruled in June that not enough progress had been made in transforming Russia's anti-doping programme, but Shubenkov said the ban does not protect the rights of clean athletes.
"People who have been taking drugs anywhere should be punished and I have no tolerance for them, but today I am punished and I am a clean athlete," Shubenkov told the BBC.
"No-one cares that my career is going to be ruined... Before it was like if there are any cheaters coming (to Rio) then they are going to deprive clean athletes of a chance to win.
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"But now the clean athletes are deprived even of the chance to go and compete and this is okay? To my mind, this is unhealthy."
The 25-year-old Russian, who revealed his application to compete in Rio as a neutral athlete was turned down by the IAAF, said he has never taken drugs. "Re-test me anytime you want, come to me everyday. I am ready to do anything," he said.
The McLaren report into Russian doping, published on Monday, revealed evidence of a systematic and widespread state-sponsored doping by Russian athletes at the 2014 Sochi Winter Olympics.
That led the World Anti-Doping Agency (WADA) to recommend extending the Rio Games ban to all Russian athletes and not just in track and field.
Russia's participation in Rio is hanging in the balance after the International Olympics Committee said on Tuesday it would "explore legal options" for banning the country from the Games.
(Reporting by Shravanth Vijayakumar in Bengaluru; Editing by Toby Davis)
