Vladimir Putin said it is "unjust and unfair" that the ban on Russian athletes imposed for systemic doping was upheld by the sport's governing body, ruling out the country from competing in track and field at the Rio Olympics.
Despite desperate attempts by Russia to get the ban lifted before the games in August, the International Association of Athletics Federations (IAAF) voted unanimously against lifting the prohibition.
Reacting to the news publicly for the first time, the Russian president told a press conference in St Petersburg: "Of course that is unjust and unfair.
"There are universally recognised principles of law and one of them is that the responsibility should be always personified - if some of the members of your family have committed a crime, would it be fair to hold all the members of the family liable including you? That is not how it's done.
"The people who have nothing to do with violations, why should they suffer for those who committed the violations? That actually does not go into the framework of civilised behaviour."
Russia's track and field team was banned from competing after a report by an independent commission chaired by former World Anti-Doping Agency (WADA) president Dick Pound found evidence of a state-sponsored doping ring that it said sabotaged the 2012 London Olympics.
But Mr Putin insisted the government is trying to crack down on doping, and was not behind it.
"We feel indignation ourselves when we face the problems of doping and we try to cut this and punish the culprits," he added.
"But the so-called clean athletes, why should they suffer? That is not understandable to me.
"I hope that we will be able to find some solution here, but of course that does not mean we are going to be offended and say we are not going to fight doping. No. We will make the doping fight fiercer."
Mr Putin also alluded to the controversy surrounding the "notorious meldonium", the substance which saw Russian tennis player Maria Sharapova fail a drugs test and land a two-year ban.
"What is considered to be doping? Doping is medicine which gives you [an] advantage in competing," he said.
"Meldonium does not give this advantage - it just keeps your heart muscle healthy during the extreme loads and for many years it was not considered to be doping.
"But everyone has known that meldonium was invented on the territory of the Soviet Union, it was taken only by athletes from Eastern European countries - everyone knew that well.
"Why do they have to single out this very substance?"
Sharapova was suspended by the International Tennis Federation for two years after she tested positive for meldonium at this year's Australian Open.
The tennis player claimed in March she was prescribed the drug in 2006 for "several health issues" and was unaware it had been added to the prohibited list at the turn of the year.
Mr Putin said there was little consensus about how long it takes for meldonium to leave the body, adding that he felt the decisions made were "hasty".
"But we believe that everyone makes mistakes and our partners could have made a mistake as well," he added.
"No one should be deemed liable of those who did not commit any violations, so I hope we do have some more conversations with our colleagues in WADA, and I do hope that we receive the proper response from the International Olympic Committee."