The plaques are approximately 6in by 8in with a small wooden cross on the top edge.
John Muir, the Secretary of the Italian Chapel Preservation Society, said the theft of the of the plaques was "devastating".
The church has since become a major Orkney tourist attraction drawing more than 90,000 visitors a year.
The prisoners were held in what was designated Camp 60, which comprised 13 huts on the uninhabited island of Lambholm. Several hundred PoWs were put to work on a major construction project to shore up the defences of Scapa Flow.
Four concrete causeways linking four islands - the Churchill Barriers - were built on the orders of the wartime prime minister to stop German U-boats from attacking ships at anchor in Orkney's natural harbour.
The Italian prisoners were given two Nissan huts in 1943 to convert into a place for them to worship. They led by one among them Domenico Chiocchetti, a gifted painter who had been captured in North Africa.
Before the chapel was built Chiocchetti, produced a statue of St George fashioned from barbed wire and covered with concrete. The prisoners also worked to build a theatre and a recreation hut. But today the chapel and Chiocchetti's St George are all that remain of Camp 60.
In 1964 Chiocchetti returned to Orkney with his wife to make a personal gift to the chapel of 14 panels of the Stations of the Cross hand-carved in Cirmo wood. There was also a gift from the mayor and community of Moena, where he was from, of a standing crucifix and altar cruets of Venetian glass.
Police are asking anyone with information to get in touch.