One of Rome’s most enduring mysteries – the 1983 disappearance of 15-year-old Emanuela Orlandi, a Vatican employee’s daughter – took a new twist on Saturday when papal authorities announced that they had discovered two sets of bones under a stone manhole.

On Thursday the Vatican had pried open the tombs of two 19th-century German princesses in the cemetery of the Pontifical Teutonic College after Emanuela’s family had received a tip that her remains might be buried there. But the tombs turned out to be completely empty, creating yet another mystery over the whereabouts of the dead princesses.

The Vatican pledged further investigation and on Saturday a spokesman said they had “identified two ossuaries, located under the pavement of an area inside the Pontifical Teutonic College, covered by a manhole”.

He said the area had been sealed off and would be opened for forensic experts to investigate this week.

The last recorded structural work at the college and its cemetery was in the 1960s and 70s. Orlandi disappeared in 1983 after leaving her family’s Vatican City apartment to go to a music lesson in Rome. Her father was a lay employee of the Holy See. Over the years her disappearance has been linked to everything from the plot to kill Pope John Paul II to the financial scandal of the Vatican bank and Rome’s criminal underworld. The last major twist in the case came in 2012, when forensic police exhumed the body of a reputed mobster from the crypt of a Roman basilica in hopes of finding Orlandi’s remains as well. The search turned up no link.

Last year bones were found underneath the Vatican’s embassy to Italy in Rome. Italian media immediately speculated the remains could belong to Orlandi or another girl who went missing around the same time. But forensic tests showed the bones long pre-dated their disappearances.