"This drug has nothing to do with doping," Putin said during an annual call-in show. "It does not impact results at all. It simply keeps the heart muscle in good condition under high strain."
Since tennis star Maria Sharapova admitted last month that she tested positive for meldonium at the Australian Open, a number of high-profile Russian athletes - including Olympic swimmer Yulia Efimova - have also tested positive for the drug.
Russian sports minister Vitaly Mutko said earlier this month that 40 Russian athletes had tested positive for the drug since a World Anti-Doping Agency (WADA) ban came into force on January 1.
Putin said he did not think WADA's decision to ban the drug, first produced in Latvia during the Soviet era, had "political implications".
Other Russian officials, including Foreign Minister Sergei Lavrov, have hinted that the ban on meldonium unfairly targets athletes from the former Soviet Union, where the drug is widely available.
WADA, which said Wednesday it had recorded 172 meldonium case since the substances was banned, declared that athletes could escape a ban for taking meldonium because it does not know for sure how long it takes the substance to leave the body.
WADA also said action could be suspended if between one and 15 micrograms of meldonium are detected and the test was taken before March 1. The agency said this is because studies are needed to determine when a substance was taken.
In a separate scandal a report by a WADA independent commission published in November alleged state-sponsored doping and mass corruption in Russian athletics, prompting the International Association of Athletics Federations (IAAF) to provisionally suspend Russia.
The IAAF is expected to make a decision on Russia's participation in the Games next month.