Ettore Gotti Tedeschi feared for his life because his efforts to crack down on alleged money laundering and making the bank's operations more transparent had targeted accounts held by mafia godfathers, the Italian media reported.
The banker was preparing to send a copy of a dossier of letters, emails and other documents that he had compiled to Monsignor Georg Ganswein, one of Benedict XVI's two private secretaries.
He had also requested a private audience with the Pope a few days before he was ousted by the board of the bank on May 24 after three years at the helm of the institution.
He left instructions with his secretary to send two other copies to a lawyer and to a prominent Italian journalist, with notes saying that if anything happened to him, the explanation would be found within the documents.
The secret dossier consisted of 47 binders of documents, including some which related to Mr Gotti Tedeschi's efforts to convince Cardinal Tarcisio Bertone, the Vatican secretary of state and de facto prime minister, of the need to clean up the bank's activities so that the city state could join an international "white list" of financially transparent countries.
Cardinal Bertone allegedly tried to water down some anti-money laundering regulations that Mr Gotti Tedeschi, 67, wanted to adopt, and engineered the banker's dismissal.
The Vatican has denied the allegations and has claimed that it was in fact Mr Gotti Tedeschi who was dragging his feet on the reforms.