A total of 46 dead waxwings were found dead on 15-18 March, with head injuries, broken bones, ruptured internal organs and crushed chests in southeast and northwest Moscow.
"Experts from the Russian Birds Conservation Union believe the bird deaths could have been caused by mirrored windows," the department said in a statement. "Waxwings may have lost their bearings and banged into walls and windows."
It was earlier reported that the birds could have been shot, but an autopsy has refuted this theory.
"The suggestion that the birds could have died from fermented rowan berries also proved to be false, as they contain less than 0.5% of alcohol," the statement says.
Two of the three birds, which were found alive, died late on Thursday and their bodies were sent for tests to rule out the possibility of disease.