"We are creating a new system of fighting against doping," News agency TASS quoted Putin as saying.
"We will transfer this system from the sports ministry to an independent organisation, as has been done in many countries in the world," he said.
He said that a new laboratory is to be built on the grounds of Moscow State University.
Russia has been pondering reforms since an investigation by the World Anti-Doping Agency (WADA) revealed evidence of state-sponsored drug cheating that saw its athletics team and entire Paralympics squad sidelined from the Rio Games last year.
Putin admitted that Russia's previous anti-doping system was ineffective, but denied outright the existence of a state-run doping program in the country.
Meanwhile, Michael Phelps, the most decorated Olympic athlete of all time who retired after last year's Rio Games, told US lawmakers investigating doping on Capitol Hill that the International Olympic Committee (IOC) should make more resources available to WADA.
"In my opinion this is something that needs to be handled today," Phelps told the House Energy and Commerce subcommittee on oversight and investigations.
"We need to find whatever the way is to figure out this issue. If that's more money, it's more money," Phelps added.
Questioned on how long it would take to achieve reform, Phelps could not offer a timeframe but warned that doping scandals were "crushing" sport.
United States Anti-Doping Agency (USADA) chief Travis Tygart meanwhile pinpointed the overlap between the IOC and WADA as part of the problem, calling for a clean separation of powers between the two bodies.
However the IOC's medical director Richard Budgett told lawmakers the Olympics movement was already addressing the reforms called for by Tygart.
"The IOC is in the process of removing the fox from the hen house," he said.
But Tygart commented that he hasn’t seen anything moving. "We're still waiting," he says.
The USADA chief proposed that the IOC and WADA could take immediate steps to begin the reform process while “funding a properly resourced anti-doping regime.”