The mosques in Gaza City and Khan Yunis were closed to worshippers on Friday morning, the ministry said, Safa news agency reported.
They will remain shut for 48 hours before a decision is made about whether or not to reopen them, it said.
Meanwhile, two mosques in Rafah city in the southern Gaza Strip that had been closed for coronavirus concerns have been reopened.
Coronavirus cases among the general population are rapidly increasing in the Gaza Strip as over two hundred infections are being discovered daily.
The first community spread of the deadly virus was detected in late August and over eight thousand cases have been discovered so far.