It said this accounts for 24 percent of the total number of mosques in the North African country.
In the first phase, those mosques allowed to reopen will open their doors to worshippers 15 minutes before every prayer and close ten minutes after the prayer, the ministry said, el-messa news website reported.
It also underlined the need for observing the health protocols to prevent the spread of the coronavirus.
Algeria said on Saturday it will further ease its coronavirus lockdown, including shortening an overnight curfew, lifting some travel curbs and allowing large mosques to reopen.
The use of air conditioners in mosques remains banned, as does a prohibition of access for women, vulnerable people and children under 15 years, the government said.
The North African country has recorded 35,160 coronavirus infections, with 1,302 deaths.
In June, it resumed some economic activity, mainly in the construction and public works sectors, and allowed the reopening of some businesses.