The historic chapel built by Italian prisoners during the Second World War, has become a major tourist attraction, drawing more than 90,000 visitors a year.
But police are now investigating after the plaques, which form part of a set depicting the journey of Christ to the cross, were stolen from inside the building, which is left open during the day.
The artefacts are believed to have been taken some time between July 28 and Tuesday this week. Police are asking people who visited the chapel between those dates to contact them with any images of the interior to help narrow down the time of the theft.
It is the second time the chapel has been the subject of criminal attention this year after it was one of the targets of a series of break-ins in Orkney in May.
John Muir, secretary of the Italian Chapel Preservation Society, said yesterday: "It is really devastating news. I would have thought it would be very unlikely they were taken by anyone resident in Orkney.
"If they have gone out of the county I can't see if they will ever be returned."
Mr Muir said that the plaques would not necessarily be worth much money. "I don't think anyone on the open market would want to pay a great deal for them," he said. "But they are of great sentimental value to the chapel."
The Italian prisoners of war were held in what was designated Camp 60, which comprised 13 huts on the uninhabited island of Lamb Holm. Several hundred were put to work shoring 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 keep out German U-boats. They now carry the inter-island road.
The Italian prisoners were given two Nissen huts in 1943 to turn into a place of worship. They were led by a gifted painter, Domenico Chiocchetti, who like others had been captured in North Africa.
Before the chapel was built, Chiocchetti produced a statue of St George fashioned from concrete.
The prisoners also worked to build a theatre and a recreation hut, but today the chapel and the statue of St George are all that remain of Camp 60.
Chiocchetti, who died in 1999, returned in 1960 and again in 1964, when he travelled to Orkney with his wife to make a personal gift to the chapel of 14 hand-carved wooden of the Stations of the Cross. There was also a gift from the mayor and community of Moena, his birthplace, of a standing crucifix and altar cruets of Venetian glass.
The plaques, made of mahogany, are approximately six inches by eight inches with a small wooden cross on the top. Each plaque shows an image of Christ.
Mr Muir said: "We have been celebrating the 70th anniversary this year of the chapel and it is very disappointing that this is the second event of this sort to happen.
"The chapel is open during daylight hours, but there is not a custodian on duty all day. We lock the chapel at night. We have many thousands of visitors going through each year, in fact last week we had 7500."
Local councillor Andrew Drever, a member of the Chapel Preservation Committee, said: "Given that this building is freely open to all, through a position of trust, it is very disappointing that such an internationally well- respected monument has been raided of these artefacts.
"This year we are commemorating the chapel's 70th anniversary and this action, together with a break-in earlier this year, make it all the more deplorable.
"Our Italian Chapel is above all a symbol of peace and reconciliation. I would appeal to whoever removed the carvings to return them immediately to their rightful place, either in person or anonymously."
A spokesman from Police Scotland said: "Police in Orkney would like to hear from anyone who may have taken digital photographs of the chapel interior between the dates given. This will help to narrow down the time-frame for when the theft occurred."
Last month it emerged two companies were in talks about making films about the chapel.