The statistics released by the health department showed that Moscow recorded over 5,700 more deaths from all causes in May than the average for the previous three years.
Moscow's health department said in a statement that 5,260 of those people had died from coronavirus.
The figure is substantially higher than the official death toll for Moscow published by Russia's national coronavirus response center, which stands at 3,083 deaths since March.
Russia's official coronavirus statistics have been the subject of controversy. The release last month of similar mortality data for April also showed Moscow's official coronavirus death toll was significantly lower than the number of extra deaths recorded that month compared to previous years.
Experts around the world have said counting such "excess" deaths represent the best way to estimate the real toll of the pandemic, given the widely divergent way of recording COVID-19 deaths between countries.
Moscow's authorities initially rejected that approach when it was applied by analysts last month, insisting their numbers were not an undercount. The city's health officials said the death toll was low compared to other countries because Russia was only including deaths where COVID-19 was determined to be the direct cause.
Medical experts and health workers have questioned that method as potentially too narrow and critics have accused authorities of using it to present a rosier picture of Russia's epidemic.
Moscow's health department appeared to respond to the criticism, saying it was now also including deaths where the virus had been determined to have exacerbated underlying medical problems.
The department said it could do so following "new recommendations" from Russia's health ministry.
Even with the new numbers added, Moscow's death toll appears lower than other major global cities.
Based on the new figures, Moscow -- with a population 12 million -- had a COVID-19 mortality rate of 3.8%. That compares with 12.5% for Madrid, where 8,691 have died, or 9.5% for Rio de Janeiro, where 6,928 have died, according to data from John Hopkins University.
Experts caution comparing mortality rates across countries is largely unworkable currently given the wide variation in how countries record COVID-19 deaths. But excess deaths for other major cities were also much higher than Moscow's. London recorded 9,700 excess deaths during the worst period of its epidemic, according to an analysis by The Financial Times, a 130% jump. New York's was over 200% higher.
"Compared to most cities of that size, Moscow survived better," Alexey Raksha, an independent demographer in Moscow, told ABC News, based on the data currently available.
Moscow's health system, while seriously strained, has never appeared to be totally overwhelmed as in northern Italy. Doctors have said many hospitals were full, but the city had not run out of beds.
"All cities of the world went through these periods differently; most were faced with a real tragedy. In Moscow, it went rather smoothly," Moscow Mayor Sergey Sobyanin told the Interfax news agency. "Nevertheless, it can now be said that the number of deaths was quite high in May. It's less than in many cities of the world, but it's still high."
Demographers have suggested several factors for why Russia, and other eastern European and former Soviet countries, appear to have done better than some Western countries. Some have suggested Russia's lower life expectancy means it has fewer elderly citizens, the most vulnerable to the virus. Russia's health system, inherited from the Soviet Union, also is geared to infectious disease epidemics, and so it has more hospital beds.
Moscow's new numbers are raising questions about Russia's official coronavirus statistics overall. Officially, the country has one of the lowest mortality rates in the world for coronavirus, at 1.5%. It has recorded just 6,350 deaths from over 490,000 confirmed cases, according to Johns Hopkins.
Mortality data for May in St. Petersburg -- Russia's second largest city -- showed it recorded over 1,400 more deaths than usual that month. But the city's official coronavirus death count stood at just 171.
Raksha, the demographer, said the official death count published by Russia's coronavirus response center clearly also still did not include deaths indirectly caused by COVID-19.
He called using the figures to calculate a real mortality rate was "almost useless," or at least "much more difficult."
Some demographers have also warned there are signs undercounting by regional authorities is accelerating after the Kremlin signaled the country should move out of lockdown.
The government has been encouraging regions to begin lifting restrictions, even as the epidemic continues to grow outside of Moscow. Russia has registered around 9,000 new cases per day steadily for the past few weeks, even after the growth rate stabilized.
Some are attributing the haste to reopen to the Kremlin's determination to hold a referendum this month on constitutional changes that would allow President Vladimir Putin to remain in power until 2036.
After Putin announced the referendum would go ahead, Sobyanin abruptly reversed his position that lockdown measures would need to remain in place for weeks more. On Monday, he announced the lockdown was over and he was lifting most restrictions the next day.
Following Putin's announcement, Russia's health ministry also said it would no longer include asymptomatic cases in its national coronavirus total. In Moscow, the daily number of new cases recorded has suddenly fallen by several hundred in the three days since Sobyanin announced the lockdown was over.
In Moscow, the unexpected release and declaration of victory over the epidemic has prompted jokes online.
"Scientists around the whole world are fighting to create a cure for coronavirus. It turns out we just needed to set a date for a vote on changes to the constitution," Tikhon Dzyadkov, editor in chief of the liberal channel TV Rain, wrote on Twitter.