A man is under arrest after being caught red-handed vandalising the main staircase at the palace in Valletta.
The incident happened on Tuesday afternoon.
"The man, employed by a contractor to carry out cleaning duties at the Palace, was caught drawing graffiti on a part of the wall of the round staircase and on balustrades located in the same stairway," Heritage Malta said.
An investigation has been launched.
Conservators from Heritage Malta and other professional staff established that furniture varnish was used in the vandalism.
"Preliminary assessments suggest that no permanent damage has been caused, and restoration efforts are already underway," the agency said.
The palace, originally used by the grand masters and now the seat of the President, was reopened to the public in January this year following an extensive restoration project.
In April, an architect involved in the restoration of the palace was taken to court and accused of stealing three antique vases and a clock from the historic Valletta building.
Ljubica Zivkovic, 52, from Belgrade, Serbia, denied the charges of aggravated theft, unlawful possession of the cultural artefacts acquired illegally and breaching probation for similar offences.
In May a pensioner who ran a pawnbroker's shop was charged with possession of the stolen items. He pleaded guilty and was handed a two-year jail term suspended for four years.