Losses included a controversial $20.5 million loan granted to a production company owned by a friend of Cardinal Tarcisio Bertone, the former Vatican secretary of state who has faced criticism for mismanagement as the church's No. 2 official under retired Pope Benedict XVI.
The number of bank customers dropped from 18,900 in 2012 to 17,419 last year and has continued to fall this year. Around 3,000 accounts were closed, including 2,600 that were considered dormant.
In recent years, the bank has faced increasing pressure from European officials and the Bank of Italy to shed its reputation as an offshore haven and to adopt international guidelines designed to prevent money laundering and terrorist financing.
The bank said it has stepped up transparency and moved to restrict account access to Catholic institutions and clerics, Vatican employees and embassies and diplomats accredited to the Holy See in a bid to tighten control.
"I repeatedly said that I would proceed with zero tolerance for any suspicious activity," bank President Ernst von Freyberg said in a statement. "We have carried out our reforms in this spirit."
The bank released the new figures amid speculation that its board will be restructured and von Freyberg will be replaced Wednesday. French businessman Jean-Baptiste de Franssu is expected to succeed von Freyberg; both men are due to attend a news conference with the Vatican's economic overseer, Australian Cardinal George Pell.
"This is a time of major change in the Holy See, not only for the [bank]," Pell said. "With the support of the Holy Father and the Council of Cardinals, we are creating simpler, more efficient structures for those serving the mission of the Catholic Church."