Three vases and a clock costing €13,000 have gone missing from the Grand Master's Palace, Heritage Malta said on Friday.
In a statement, the national agency said the items went missing from halls within the palace. Their disappearance was flagged by Heritage Malta officials.
The agency filed a report about the missing items with the police, which in turn launched an investigation.
The police and Heritage Malta officials are reviewing footage caught by the CCTV system at the palace.
The Valletta palace was reopened to the public earlier this year following five years of intense restoration that has more than doubled its accessibility to visitors.
The disappearance of the vases and the clock comes less than a month since two gold medals valued at €400,000 were stolen from the Maritime Museum in Vittoriosa.
The medals were traced inside the residence of a man who was arraigned over their theft and granted bail.
Justin Mallia, 25, from Cospicua allegedly posed as an official from the education department, visiting the museum to deliver documents, when he stole the gold medals to settle debts.
The museum has since beefed up security and launched an internal probe.