Pope Francis has sought to stamp out corruption and other abuses at the bank, which handles the Church’s funds.
The news comes after the bank said its profit fell to 2.9m euros (£2.3m) in 2013, down from 86.6m euros in 2012.
Attempts to create a more transparent banking system for the Catholic Church, begun by Pope Benedict after allegations were made that the Vatican bank had been used by money launderers, will continue under new management.
Balance sheet woes
The Vatican’s precarious financial situation was revealed by the simultaneous publication in Rome of balance sheets for 2013 of the Holy See, of the Vatican City state, a separate entity, and of the Vatican bank, known officially as the Institute for Religious Works (IOR).
The IOR moves money around the world to finance Catholic missions and provides banking services for the pope, clergy and religious orders.
Alongside the bank’s massive drop in profits, the Holy See, the administrative headquarters of the Church, ran up a deficit of 24.2m euros (£19.2m) last year.
However Vatican City state, the tiny sovereign enclave in the heart of Rome, which derives a large part of its income from tickets to the Vatican museums, reported a profit of 32.3m euros (£25.7m).