The Ara Pacis altar, dating to 9 BC, has been flooded after the museum's modern glass-pannelled roof failed to withstand the torrential rain on the night of Tuesday 19 November.
The leak was only noticed the following morning, despite the presence of night staff, according to Rome daily newspaper Il Messaggero.
Rain water lodged on top of the ancient monument, as well as flooding its internal section. Conservation staff used tarpaulins and buckets to drain the monument and the surrounding areas, drying the floors with cloths and vacuum cleaners.
The cause of the leakage is believed to be poor maintainence of the roof of the museum which was designed by American architect Richard Meier and inaugurated in 2006.