The safe was taken from the director's office of the Catacomb of Priscilla, located on Via Salaria in central Rome, in the early hours of Sunday morning.
It contained documents belonging to the religious association which runs the catacombs on behalf of the Vatican, Il Messaggero reported.
The alleged thieves gained access through the adjacent Benedictine convent of Priscilla, breaking a glass door to enter the catacomb, which is not equipped with an advanced anti-theft system.
Once inside, they rampaged through several rooms before finding the safe and fleeing with it.
Evidence of the break-in was discovered by Benedictine nuns on Sunday morning, who were reportedly 'shaken' by the burglary.
The mother superior refused to speak to the press about the incident.
Police fingerprinted the crime scene on Sunday and are reviewing CCTV footage to try and identify the thieves.
One hypothesis is that they were specifically commissioned to steal the safe for its contents, but the possibility that it was a random burglary, undertaken by burglars looking for valuables, has not been ruled out.
The Catacomb of Priscilla is located in an ancient Roman quarry and dates back to the second century. It is one of the world's most important early Christian catacombs, a place where several martyrs and no less than seven popes were buried.