CAIRO — After an electrical fire raced through a tiny Coptic Orthodox Church in central Cairo on Sunday and killed 41 worshipers, President Abdel Fattah al-Sisi of Egypt ordered the army to renovate the building immediately.

Under the watch of soldiers, dozens of laborers worked throughout the night, dragging out charred beams and broken pipes, and repainting the walls and the iron cross atop the narrow four-story building wedged between shops and apartments. By Monday evening, the exterior of the Abu Sefein church, at least, looked newly built.

The government also offered condolence payments.

But that quick action did not stop the patriarch of Egypt’s 10 million Coptic Orthodox Christians from venting frustration on Tuesday that the Middle East’s largest Christian community has been squeezed by decades of government regulations restricting the number and size of churches in this predominantly Muslim country.

“The restrictions led to the construction of small churches that do not correspond to the Christians’ needs,” Pope Tawadros II said Tuesday in an unusual statement of implicit criticism. He called on authorities to either move the 12,000-square-foot Abu Sefein church to a larger space or allow it to expand it to accommodate the large numbers of Christians in the neighborhood.

His statement was softened by praise for the response by Mr. Sisi and civil defense forces and noted that the restrictions began under previous governments. But in a country where any criticism of government by Christian officials is exceedingly rare, it still spoke volumes.

Among the 41 dead were 18 children and the bishop who was conducting the Divine Liturgy when the blaze broke out at the church in the working-class neighborhood of Imbaba. Most died from smoke inhalation or were trampled while trying to make their way from the fourth floor, where the service was held, to the ground floor exit, a spokesman for the Coptic Orthodox Church, the Rev. Moussa Ibrahim, said Tuesday.

Some of those who survived escaped through the windows or rooftop.

Father Ibrahim said that about 100 people were gathered for the Sunday service when the fire started, meaning nearly half of all those in attendance had perished. Church officials had originally said up to 500 were present at the time of the fire.

The interior ministry is still investigating the cause of the fire. But church officials said it began shortly after a generator there kicked in during a power outage. The generator exploded when the power came back on during the Sunday service.

“The fire affected the entire electrical network and the smoke was everywhere,” said Father Ibrahim, the Coptic Church spokesman, adding that the entire electrical system had short-circuited at the same time.

The semiofficial Al-Ahram newspaper said the government renovation after the fire included some upgrades to the electrical system with the installation of higher-capacity cables.

Father Ibrahim denied a witness report that the main door of the church had been locked at the time of the fire, preventing worshipers from escaping.

Coptic Christians trace their roots to the ancient Egyptians, and the country’s churches are a mix of cathedrals that resulted from grand government gestures of solidarity, and tiny, makeshift churches in poorer areas.

Electrical fires broke out at two other Coptic churches in Egypt on Monday and Tuesday, one in Cairo and the other in Minya province a few hours to the south, according to government and local officials. There were no reports of casualties. The church in Minya, which a church official said was empty at the time, appeared in videos to be heavily damaged.

But the three fires in as many days reflects the general state of disrepair in buildings across Egypt, where there is often substandard construction and little enforcement of safety standards.

Cairo, the Egyptian capital, is one of the most densely populated cities in the world, and the Imbaba neighborhood is made up of narrow streets packed with shops and apartment buildings overlooking a tangle of street vendors.

The Abu Sefein church had operated unofficially until after 2016, when its status as a church was legalized, Father Ibrahim said. That same year, Mr. Sisi passed a law removing many restrictions on building and renovating churches, but it left much of that power to the whims of local government officials, who can block permits for churches.

Ishak Ibrahim, a researcher at the Egyptian Initiative for Personal Rights, said Abu Sefein was licensed in 2019, but because it was not purpose-built and was limited in size, the church expanded upward.

The U.S. State Department 2021 report on religious freedom in Egypt noted that the size of new churches allowed depends on a government determination of the “number and need” of Christians in the area. It said building of churches is subject to more government scrutiny than the construction of new mosques.

Egypt has historically been one of the major centers Sunni Islam in the region. At a wake on Monday in a church hall for three children killed in the fire, the call to prayer from a nearby mosque’s loudspeaker drowned out the priest’s sermon.

Tension between Christians and Muslim communities in Egypt has been focused largely in rural villages, many of them in Minya province, which has the highest percentage of Christians in the country. In some villages, Christians denied approval by local governors to construct churches are left with nowhere but the streets to hold religious services for funerals and weddings, according to Christians in Minya.

Maj. Gen. Mohamed Nabil Omar, a former civil defense director, said all places of worship as well as other buildings were required to have emergency exits, as well as safety inspections every one to three years.

Neither government nor church officials would comment on any findings of the investigation so far, or on whether or when the building’s wiring had last been inspected.

“If the government decides today to close off all buildings deemed unsafe according to official reports, three-quarters of Egypt will be closed down,” said General Omar.

Nada Rashwan contributed reporting from Cairo.