Archbishop Vincenzo Paglia is alleged to have colluded with the local council to buy the building at a low price using diocese funds.
It's claimed the clergyman then planned to use the building in Umbria as a guest house or for a Church purpose before selling it on for a profit of around £3 million.
San Girolamo castle was sold four years ago for around a third of its true value, prosecutors alleged.
Archbishop Paglia is head of the Vatican's Pontifical Council for the Family and a senior figure in the Pope's team in Rome.
Authorities said nine other people were being investigated including a former mayor and two members of staff of the Diocese of Terni.
In a statement the archbishop denied the allegations: "I remain at the disposition of the investigating authorities and I have full confidence in the justice system".
Vatican spokesman Fr Federico Lombardi said: "We at the Vatican have nothing in particular to say about this affair. We trust that the magistracy will do its work well."