Museum Director Ioannis Eliades said no monetary value can be put on the items including fragments of a 1,500-year-old mosaic depicting a clean-shaven St. Thomas and 1,100 year-old frescoes of unidentified saints.
The frescoes, from the church of Saint Solomone in the village of Komi tou Yialou, are the oldest of their kind in Cyprus which traces its roots in Christianity to the 1st century.
The Apostle Paul is said to have preached the gospel in A.D. 45 and converted the island's Roman governor Sergius Paulus, the first head of a Roman territory to undergo conversion.
Other important works include the 14th century icons of the Virgin Mary the Merciful from the monastery of Saint John Chrysostom in the village of Koutsoventis and a 16th century icon of Saint Mark from Saint Andronikos Church in Kythrea village.
Police discovered the religious treasures in a 1997 raid on the apartment of Turkish art dealer Aydin Dikmen in Munich, Germany. The treasures remained in the custody of German authorities until a protracted court battle could prove the Cyprus Church's ownership.
"I'm touched that such a large quantity of religious treasures have been returned," German Ambassador to Cyprus Gabriela Guellil told The Associated Press.
The church says hundreds of religious artifacts were looted from churches in the island's north and many have appeared on the black market in Europe, the U.S. and Asia.