Mosques and churches will not be allowed to hold their weekly main services, when large crowds traditionally gather for worship.
The government has also banned Friday prayers at mosques and Sunday Masses at churches, Madbouly said.
Health protocols should also be observed and measures such as sanitizing the places of worship and maintaining social distancing is a must.
Egypt has so far reported 62,737 coronavirus cases. COVID-19 has killed 2,620 people in the country.