The model is equipped with the same navigation system installed on the Boeing-737 that crashed on a Siberian railroad track linking Russia's Yekaterinburg and Perm, killing all 88 people on board, on September 14.
"We have sent telegrams to a number of Russian air companies, in which we are not just recommending, but categorically prohibiting the use of Boeing-737-500 VP-BKT aircraft," a spokesman for the agency said.
He said the telegrams had been sent to six air companies, including Aeroflot-Nord, Aeroflot-Don and Volga-Dnepr, and the ban would remain in force until pilots from the airlines undergo additional training.
One of the theories put forward for the crash is that the plane's pilots were unfamiliar with the indicators on the navigation system.
The Boeing-737-500, owned by flagship Russian carrier Aeroflot, crashed on the railroad only 300-500 meters (1000-1600 feet) away from residential buildings. The wreckage was scattered across an area of 10 square km (4 square miles).( Boeing-737-500 crash kills 88 - Image gallery)