The church, on an island in Lake Van, was damaged during the mass killing of Armenians during the First World War.
It was restored by the government in 2007 and turned into a museum.
Turkey has allowed the Mass to take place in the hope that it will be seen as a gesture of reconciliation, but some have denounced the move as a publicity stunt.
Hundreds have travelled from around the world to listen to the ancient Armenian Gregorian liturgy in the tiny 10th-Century church of the Holy Cross on Akdamar island.
However, numbers are much smaller than the local government had predicted.
ConcessionMany Armenians have chosen not to come, seeing this as an inadequate step from a government which still refuses to acknowledge the mass killings of Armenians in this area as a genocide, says the BBC's Jonathan Head at the church.
Nonetheless, for those who are here, it is a very moving occasion and they certainly believe that this is a positive step forward, our correspondent says.
This region of Turkey was once mainly populated by Armenians.
Turkey is still tightly controlling all forms of religious expression and the government is only taking timid steps, fearing a nationalist backlash if it is seen to be making too big a concession towards the Armenians.
Hundreds of thousands of Armenians died in mass killings and deportations by Ottoman Turk forces in 1915-16.
Armenia says 1.5m people were killed in a genocide, but Turkey strongly rejects the charge, saying the number of deaths has been inflated and that the people died as a result of the strife of World War I.
SIC: BBC/INT'L