A wall next to the entrance to the Cittadella ditch as well as some of the masonry walls have collapsed as a result of the persistent rainfall.
The Gozo Ministry's Cultural Heritage Directorate said the ditch will be closed to the public until it confirms it poses no danger.
"We would also like to inform that some of the masonry walls at the perimeter of the ruins have collapsed and therefore we ask the public to be vigilant," the ministry said.
It is the latest casualty of the heavy rain and winds that hit Malta over two days. Part of Popeye Village in Mellieħa, the 17th century Għajn Tuffieħa tower and the airport VIP lounge were among those damaged by the weather.
Situated in the centre of Gozo, the historic Cittadella has been a very popular settlement location since Neolithic times. Its geological and geomorphological characteristics were ideal to support ancient settlements and provide a foundation for town development.
An extensive five-year restoration project of the site was completed seven years ago.
More to follow