The president’s comments came after international athletics bosses meeting in Vienna decided not to lift the ban on Russia’s athletics federation in time for the Rio Olympics.
Despite desperate Russian attempts to have the ban lifted before the August games, the International Association of Athletics Federations’ 27-strong council decided Russia had not met the criteria for reinstatement.
Russia has been suspended from international competition since November after an investigation commissioned by the World Anti-Doping Agency (Wada) uncovered systematic cheating.
The Wada report uncovered a “deeply rooted culture of cheating” and said samples had been destroyed and bribes paid to cover up the scam.
Asked about the allegations in a panel discussion at the St Petersburg International Economic Forum, Mr Putin said: “At the state level, we have been fighting doping in the sport and we will continue doing that.”
He added: “Anyway, the law enforcement agencies have to treat all the violators in the same way, this is our position. We are going to work in this way in our fighting against stimulants and dopers, and we are going to work with fans’ associations.
“And I believe there are many sensible people among the fans who realise that any violations cannot express their support for the team they love – any violations only jeopardise the teams they support.
“I realise that we still have a lot to do in this area. But let me emphasise that we have never supported any violations in sport, we have never supported it at the state level, and we will never support this.
“We will never support any dopers or any other violations in this area, and we are going to co-operate with all the international organisations in this regard.” He added: “I thought that if samples are taken they are always removed for storage to the international organisations and we do not affect them in any way.
Mr Putin, who has been photographed playing ice hockey, said doping undermines sport.