At least 421 civilians died in Wednesday's violence, ministry spokesman Mohammed Fathallah said.
He said 137 people had been killed in the main Rabaa al-Adawiya camp which pro-Morsi protesters had occupied for weeks.
At the smaller of the two encampments in Nahda square, 57 people were killed and 227 died in the rest of the country, he said.
The interior ministry said 43 policemen had also been killed.
The Brotherhood remained defiant on Thursday, with spokesman Gehad al-Haddad saying demonstrations would continue.
"We will always be non-violent and peaceful. We remain strong, defiant and resolved," he tweeted.
"We will push forward until we bring down this military coup."
Morsi loyalists have insisted that their demonstrations are exclusively peaceful, but an AFP reporter saw several protesters carrying weapons at Rabaa on Wednesday.
The violence prompted vice president and Nobel laureate Mohamed ElBaradei to resign, saying he was troubled over the loss of life, "particularly as I believe it could have been avoided".
NJF/NJF