A student was on Monday fined €15,000 and handed a suspended sentence after engraving letters on a main Ġgantija doorway.
Heritage Malta said the 18-year-old Italian student was visiting the site on a school trip.
He was caught in the act by a security officer and the police were summoned to the site.
It "unreservedly condemned" the "act of vandalism", saying the student caused "irreparable damage".
The youth was arraigned during an urgent session in Gozo on Monday.
He admitted to the charges brought against him and was sentenced to two years imprisonment suspended for four years - the maximum period permitted by law.
He was also fined €15,000.
"Heritage Malta, having invested considerably over the past months in the enhancement of security at its museums and sites, voices its satisfaction at the timely intervention of the security officer involved in Monday's incident," the agency said in a statement.