Head of the council issued a statement, announcing the decision, Anadolu Agency reported.
The ban includes Friday prayers and Taraweeh prayers in the holy month of Ramadan.
It is among the steps taken to prevent the spread of the coronavirus.
The Council referred to Muslim countries such as Iran, Turkey, Saudi Arabia and Pakistan as example, which banned praying in mosques during the coronavirus pandemic.
Similar prohibition has been introduced made in Kazakhstan, Kyrgyzstan, Uzbekistan.
Tajikistan has not reported any coronavirus cases in the country so far.