The blaze started just before 9 a.m. in the Abu Sifin church in the city of Giza, where up to 5000 worshippers had gathered for Mass.
Fifteen fire engines were dispatched to put out the blaze, while ambulances transported the wounded to nearby hospitals.
An electrical fire which blocked an entrance to the church was allegedly behind Sunday's blaze, causing a stampede which killed dozens and left many more suffering from smoke inhalation.
In a statement, the interior ministry said a forensic examination showed the fire began in the second-floor air conditioning as a result of an electrical malfunction.
Smoke inhalation was the main cause of death, it said.
"I offer my sincere condolences to the families of the innocent victims that have passed on to be with their Lord in one of his houses of worship," said Egyptian President Abdel Fattah al-Sisi in a tweet.
According to a cabinet statement, families of those who died will receive 100,000 Egyptian pounds ($5,220).
Egypt's second-largest city, Giza sits across the Nile from Cairo.
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