CAIRO — At least 41 people were killed and about a dozen others injured after a fire broke out in a Coptic Orthodox church in greater Cairo as worshipers gathered for Sunday prayers, according to the country’s Health Ministry.

The blaze at Abu Sefein Church — one of the largest in the municipality of Giza — was one of the country’s deadliest in recent years. It is believed to have been caused by a faulty air-conditioning unit on the second floor of the building, which also housed classrooms, the Egyptian Interior Ministry said in a statement.

Father Mikhael Guirguis, the deputy leader of the Northern Giza archdiocese, told a church-affiliated TV station that he saw children among the dead. Another priest at a nearby church who also spoke to the same TV station said children had been moved to the top floor of the building when the fire broke out, rather than being evacuated.

The majority of the deaths and injuries were the result of smoke inhalation and a stampede as people tried to flee the burning building, the Health Ministry said. The Interior Ministry said that the blaze was under control.

Video footage from the scene that was verified by The Times showed churchgoers screaming for help from windows as thick black smoke poured out from the building. In other footage, people could be seen trapped on the church’s roof as the fire spread around them.

Some residents of Imbaba, the densely packed neighborhood that is home to the church, criticized the response of the government and emergency services. One woman said in footage shared from the scene by Al Jazeera that emergency services did not arrive for two and a half hours.

Footage from outside one of the hospitals where patients were being treated showed an angry crowd. The source of their ire was not immediately clear. Egypt’s prime minister, Mostafa Madbouly, along with other senior politicians, was visiting the injured in the hospital.

“I am closely following the developments of the tragic accident,” Mr. el-Sisi said in a statement on Twitter. “I directed all concerned state agencies and institutions to take all necessary measures.”

The country’s chief prosecutor, Hamada el-Sawy, said he had ordered an investigation into the blaze.

Egypt has been repeatedly plagued in recent years by fires that spiral into mass casualty events, drawing criticism of the government’s emergency response and as well as its fire-safety standards and regulations.

In 2002, at least 370 people were killed when a fire broke out on an overnight train speeding through the expanse of Upper Egypt and flames spread from car to car. In 2005, at least 31 people died in a blaze at a state-owned theater in the city of Beni Suef after a candle fell during a production of “Hamlet.”

In 2008, a fire gutted the Upper House of Egypt’s Parliament, injuring at least 10 people. A blaze at a garment factory near Cairo killed at least 20 people in March 2021. And two separate hospital fires — in 2020 and 2021 — killed a total of nine coronavirus patients in the cities of Alexandria and Giza.

Coptic Christians make up about 10 percent of Egypt’s 100 million population, which is mostly Sunni Muslim. The minority group is frequently the target of widespread discrimination and violent attacks, including by the Islamic State’s branch in Egypt’s Sinai Province.

Nada Rashwan reported from Cairo, Euan Ward from London and Liam Stack from New York.