Egypt's deputy prime minister and finance minister, Hazem al-Beblawi, has resigned from his post over the government's handling of Sunday's deadly Coptic Christian protest.
The resignation came as members of the Coptic Christian community began a three-day fast to mourn the 25 people killed.
About 2000 people had gathered in Cairo for an initially peaceful rally to protest against the destruction of a church in southern Egypt last month.
The rally ended in clashes between the army and protesters.
The ruling military council has ordered a swift inquiry into the violence.
"Despite the fact that there might not be direct responsibility on the government's part, responsibility lies, ultimately, with the government," state news agency Mena quoted Mr Beblawi as saying.
"The current circumstances are very difficult and require a new and different way of thinking and working."
The ruling military council, which was handed the power to govern by President Hosni Mubarak before he was ousted in the popular revolt, is in temporary charge of the country while elections are organised.
The Copts, who make up about 10% of Egypt's 85 million population, have a number of grievances against the interim administration. They say the authorities have been slow to punish radical Islamists who have attacked their churches.