In a Thursday statement, the ministry said it has asked the construction company to repair the two mosques quickly after destruction caused to them during sit-ins staged by supporters of ousted President Mohamed Morsi.
Pro-Morsi demonstrators had staged a 48-day sit-in in the vicinity of the Rabaa al-Adawiya mosque in protest at the July 3 ouster of the elected president by the army after mass protests against him.
The pro-Morsi sit-in was dispersed by security forces last week, killing hundreds of people and injuring thousands.
The Fath Mosque in Cairo's Ramses Square was also a scene of another standoff after anti-coup protesters took refuge inside the mosque to avoid deadly attacks on them by security forces in the downtown square last week.
Awqaf Minister Mohamed Mokhtar said the two mosques will be restored soon since they are among Egypt's biggest mosques.