Medical workers were dying in their hundreds — 308 according to an unofficial count by medics. Many who kept working were not getting paid long-promised bonuses until recently. Some were even earning less money because the pay rate for working with covid-19 patients was lower than for their pre-pandemic jobs, such as surgeons.

The snags in delivering Putin’s bonus promise is more than just one bureaucratic glitch. It’s about a top-down governance system with underlings terrified to act. It also helps inform some of the larger truths in Russia’s struggle to control the pandemic even as countries to the west in Europe begin to lift their lockdowns.

Putin’s centralized power structure cannot handle the crisis alone. Putin delegated much of the burden to regional officials who were frightened of drawing attention to local problems and risking Moscow’s wrath.

One way to stay under the radar could be to understate cases or deaths, analysts say. With Putin’s promised bonuses, the instinct by regional leaders — ingrained over decades — was to minimize payments, fearing trouble from Moscow if they spent too much or paid people not entitled to bonuses.

Some regional officials have even counted the minutes that medical workers spent with infected patients.

“For Putin it’s a very uncomfortable position,” said Tatiana Stanovaya, director of Moscow political think tank R. Politik. “In fact, he turns out to be dependent on regional governors. Putin asks for something, and the government is not able to implement it in the way Putin intended.”

It has left Russia on the defensive on many fronts, including with regard to its official figures indicating an unusually low mortality rate. Authorities have vigorously denied accusations that statistics are being manipulated, claiming that Russia’s low rate is a sign the government is doing a good job. But it also could be Russia’s conservative counting method.

Infected patients who die in hospitals undergo autopsies. If there are no signs of lung infection, alternative causes are listed as the cause of death.

But regional statistics on cases and deaths were unreliable, Stanovaya said.

“For example, in the Caucasus region it’s just a total mess,” she added. “The numbers they give are like a fake, nothing to do with reality. In other regions, they’re not very careful with statistics and with these tests.”

There is no hiding the strains on Russia’s health system, though.

Svetlana Munirova, a surgeon of 20 years experience at Pokrovskaya hospital in St. Petersburg, was shocked to find her April pay dropped from 50,336 rubles (around $708) to 43,996 rubles ($619) as a result of being deployed to covid-19 treatment.

She did not get her bonuses until mid-May, she said in an interview, but her basic salary is lower because an infectious-disease doctor is paid less than a surgeon.

A cardiology surgeon in the same hospital told the Novaya Gazeta newspaper last month that he was normally paid the equivalent of $1,158 a month but received half as much in April because he was treating covid-19 patients.

“I don’t know why it was so hard to pay doctors and medics despite the fact that the authorities repeatedly ordered it,” said Munirova. “All my reflections on this issue will hardly change anything. Probably, like in most cases, the money ‘got lost’ on the way.”

At government meetings, Putin has grown testier by the day.

“Listen to me. Listen carefully. We have agreed, and it was clearly and unambiguously stated, that this money should be paid for working with patients with the coronavirus infection, not for some hours or minutes they are putting in,” he said at a televised May 15 meeting with government health, defense and regional officials.

Four days later, he was nagging again. “Back in March, we made provisions for incentive payments,” he complained in a televised meeting, adding that almost all of the allocated 51 billion rubles ($720 million) had been sent to regions.

“To my knowledge, far from all those who were entitled to these payments received them,” he snapped.

On Monday, health authorities finally reported that all necessary bonuses had been paid to 153,373 medical workers.

Stanovaya said regional officials interpreted the bonus payment order as narrowly as they could: Regional governors are under pressure to prove they are doing a good job fighting the virus, so they tend to minimize the reported infections.

“Either they declare a lot of covid-19 patients, and they receive more money — but in this case the Kremlin can interpret it as a failure in fighting this coronavirus — or you will have to decrease these numbers and receive less money,” she said.

One problem is that doctors are paid bonuses only for the exact time worked with patients who tested positive — but many infected patients are asymptomatic, and tests are unreliable in up to 30 percent of cases, Andrei Konoval co-chairman of the Action union of health workers, told Echo of Moscow radio last week.

“The regulations on payments are very confusing. . . . As a result, we have chaos that may lead to more protests among medics,” he said.

In the impoverished Dagestan region in the Caucasus — a region with shortages of ventilators and protective gear — the regional health minister, Dzmaludin Gadzhiibragimov, acknowledged in an interview with local blogger Ruslan Kurbanov that more than 40 doctors in the republic had died of covid-19.

That is a major embarrassment to federal government leaders, with official statistics claiming only 27 covid-19 deaths in the entire republic.

He said the republic had recorded 13,697 cases of covid-19 and community-acquired pneumonia — although the official covid-19 count was just 3,280.

“This is why we don’t trust the statistics,” said Stanovaya.

Putin asserted Tuesday that Russia had passed the peak of covid-19 cases. The daily increase has declined from around 18 percent a day in early April to 2.3 percent Wednesday. Some regions are beginning to open up.

But a spike in new cases in St. Petersburg after holidays in early May, when many people ignored isolation and social distancing rules, indicated potential dangers.

St. Petersburg health committee deputy chairman Andrei Sarana said Wednesday covid-19 hospitalizations jumped recently from around 200 a day to 670 a day, putting doctors and hospitals under “colossal pressure.”

Natasha Abbakumova contributed to this report.