The Russian president urged officials on Wednesday not to “pretend that all is fine”. During a Government meeting, Mr Putin said: “The number of new cases is rising… and what’s most alarming – the death rate is increasing.”
It came after Russia recorded a record high of 456 daily deaths related to the coronavirus on Wednesday.
The figure has brought the country’s death toll to more than 34,000.
President Putin’s comments came as smoke was seen rising from a coronavirus hospital in Moscow.
The city’s health department said on Wednesday that the incident was caused by a loss of pressure in an oxygen tank at a building under construction.
It added that no staff or patients had been at risk.
Russia has previously experienced fires at coronavirus facilities.
In October, more than 150 patients were evacuated from a temporary hospital in October following an oxygen explosion.
Five patients were also killed in May after an overloaded ventilator started a fire in an intensive care unit in St Petersburg.
Russia’s capital is reportedly more prepared for the second coronavirus wave than other poorly funded regions.
President Putin urged his regional leaders not to hide the real severity of the situation.
During the meeting, he said: “It is completely unacceptable to pretend that all is fine.”
He added: “We went through this in the spring. We know what and how it needs to be done.”
In August, Russia registered the world’s first coronavirus vaccine Sputnik V.
Early results of the Russian vaccine suggest it could be 92 percent effective.
The Sputnik V data was based on 20 cases of COVID-19 from 16,000 volunteers.
But some experts warned that Russia’s results were rushed out too early.
In a statement Eleanor Riley, professor of immunology and infectious disease at the University of Edinburgh, said: “Whilst encouraging, I worry that these data have been rushed out on the back of the Pfizer/BioNtech announcement earlier in the week.
“The Sputnik data are based on only 20 cases of COVID-19 in the trial participants, compared to more than 90 cases in the earlier trial.”