While clerics and governments across the Muslim world will greet Ramadan this week under lockdown, working together to shut mosques and urging worshipers to pray at home, in Pakistan, some of the most prominent imams have rallied their devotees to ignore the anti-pandemic measures.

Ramadan, which begins this week, is the holy month in which Muslims crowd into mosques and fast all day, holding feasts after sundown with family and friends. Those are ripe conditions for the coronavirus to spread, and imams around the world are asking people to stay home.

But in Pakistan, pandemic or no pandemic, hard-line clerics are calling the shots, overriding the government’s nationwide virus lockdown, which began late last month.

Most clerics complied with the shutdown when it was announced. But some of the most influential ones immediately called on worshipers to attend Friday prayers in even greater numbers. Devotees attacked police officers who tried to get in their way.

As Ramadan drew closer, dozens of well-known clerics and leaders of religious parties — including some who had initially obeyed the lockdown orders — signed a letter demanding that the government exempt mosques from the shutdown during the holy month or invite the anger of God and the faithful.

On Saturday, the government gave in, signing an agreement that let mosques stay open for Ramadan as long as they followed 20 rules, including forcing congregants to maintain a six-foot distance, bring their own prayer mats and do their ablutions at home.

By the time Prime Minister Imran Khan met with the clerics on Monday, deferentially promising to abide by the deal, critics were demanding to know who was in charge during this national crisis: the government or the mosques?

“The state has become totally subservient to these clerics,” said Husnul Amin, an Islamabad-based professor and scholar on Islam and politics. “It is very difficult for the state to implement what’s best for the public good. The larger public interest is always up against the clerics. It’s completely undemocratic.”

Pakistan’s imams were empowered by the military during the 1980s, when mosques across the country churned out jihadists to fight the Soviet military in Afghanistan with the support of the United States.

While other countries tried to curb hard-line clerics’ influence after the Afghan war, recognizing the dangers they posed, in Pakistan, the powerful military continued to use them as tools of foreign and domestic policy.

But their defiance of the lockdown is exposing the limits of even the military’s control.

The military wanted the shutdown, pressuring Mr. Khan to back the measure at a time when he was reluctant and worried about the economic toll. But when the security forces tried to prevent worshipers from gathering at mosques for prayers, they found themselves under attack.

In Karachi, the largest city, scenes emerged of worshipers chasing the police through narrow alleyways, pelting them with rocks and sending several officers to the hospital.

“The military has created a monster they can no longer control,” Mr. Amin said. “They are the creation of the military, and only they could handle them. That may no longer be the case.”

By the time Ramadan approached, police officers said they were no longer willing to erect cordons around mosques to stop gatherings for prayers.

While clerics acknowledge that their mosques are perfect vectors for the coronavirus’s spread — worshipers gather to perform ablutions together before cramming into the mosques, shoulder to shoulder in supplication — they say they have to protect their bottom line: money and influence.

“We know the coronavirus pandemic is a global health issue, but religious duties cannot be abandoned,” said Maulana Ataullah Hazravi, a Karachi-based cleric.

And, he added, “mosques depend largely on the donations collected during Ramadan.”

That point — money — was high on the list of grievances that the clerics raised in their letter last week.

Worshipers open their wallets wide during Ramadan, donating millions of dollars. And in places like Pakistan, where mosques are not under the authority of the state, the money can make or break an imam and the followings they try to build, often to parlay into political power to challenge the government.

Pakistani clerics have frequently used their religious authority to get loyalists to lay siege to the capital, for example, forcing the state to change policies they disagree with.

That differs from countries like Egypt or the United Arab Emirates, where the authorities give clerics guidelines or even specific remarks for their Friday sermons.

“Clerics don’t want to lose their social and political control over society. They fear that if Muslims don’t come to the mosques, they will lose their power, their influence,” Mr. Amin said.

The clerics, observers said, may worry that if the government forces their mosques to close during Ramadan — using the pandemic, from their point of view, as a cover — it could provide an opening to finally bring them under the state’s authority.

An editorial in the prominent newspaper Dawn demanded that the clerical establishment take a back seat and let the government manage the crisis.

“This should not be seen as an affront to religion,” editors wrote last week. “Rather, it is an attempt to save the lives of the general public.”

But in private meetings with officials, clerics warned that the state would invite “God’s wrath” if it restricted prayers during Ramadan, Mr. Hazravi said — code for the political chaos that imams have unleashed in the past.

While the government has given in this time, health care workers have not. A group of prominent doctors signed their own open letter on Tuesday, urging that mosques be ordered to limit attendance to five worshipers at a time. On Wednesday, they doubled down on their warnings at a news conference.

By Wednesday evening, the virus had infected at least 10,100 in Pakistan and killed some 210 people, according to officials. Experts say that the true numbers are probably much higher and that the government is not testing enough.

The country’s bare-bones medical system, stretched during ordinary times to fight preventable diseases like polio and dengue, is now completely overwhelmed. Doctors and nurses have threatened to walk off the job unless given basic protective gear, like masks and gloves. Several have fallen ill with the virus and died.

“With Ramadan approaching,” the letter from the doctors read, “we fear that allowing large congregations in mosques will increase the likelihood of infection.”

But some of the faithful say they do not care about the science.

“Muslims wait for this month for the whole year so that they can earn maximum rewards from God by fasting and offering our prayers,” said Hazrat Ali, a worshiper in Karachi, where many mosques defied the lockdown from the start.

“If the government stops us forcibly from visiting the mosques, we will resist,” he said.