The announcement about Klishina, the 25-year-old with an exemption to compete while the rest of Russia's track and field team was banned from the Games by the International Association of Athletics Federations (IAAF), came three days before she was due to compete.
The IAAF did not explain its decision. A source familiar with the issue said the ban related to new evidence uncovered by an anti-doping probe into allegations Russia ran a systematic state-backed cheating programme.
"I can say that this may not be the last provocation. I have no words - they allowed her (to the Games) themselves ... These are some provocation moments which are being done on purpose. Its goal now is Russian sport," Mutko told TASS.
Klishina defended herself, saying she was clean and was appealing against the decision to sport's highest tribunal. The Court of Arbitration for Sport said it expected to rule on it by Monday, the eve of women's long jump qualifying round.
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The IAAF barred the entire Russian athletics team from the Rio Games in response to the doping allegations. Klishina was among 136 Russian athletes to appeal the ban and was the only one given the green light to compete in Rio.
Earlier this month, Russia was also barred from taking part in next month's Rio Paralympics, after International Paralympic Committee (IPC) said Russia's Paralympians were part of a doping system overseen by the Russian government.
Vladimir Lukin, president of the Russian Paralympic Committee, told TASS news agency that the appeal against the ban is likely to be filed at the Court of Arbitration for Sport in Switzerland, sport's highest court, by the end of Sunday.
(Reporting by Katya Golubkova; Editing by Tom Heneghan and Stephen Powell)
