Francis thanked Rene Bruelhart, 47, for his work as the director of the Financial Intelligence Authority. His replacement will be made public next week.
“I resigned,” Bruelhart told Reuters.
In a statement, the Vatican said the Swiss-born Bruelhart would end his five-year term on Tuesday.
Bruelhart's departure comes amid the fallout from the controversial police raid on AIF offices last month.
Vatican police raided the AIF's office and the Secretariat of State on Oct. 1. as part of a probe into a London real estate deal that has cost the Vatican millions. The Secretariat of State spent around $200 million to purchase a minority stake in a plan to buy a building in London's Chelsea neighborhood to convert it into luxury apartments, according to Reuters.
Five Vatican employees were suspended after the raid. Domenico Giani, Francis' longtime bodyguard, resigned over the leak of a document related to the investigation.
Vatican prosecutors are looking into whether crimes such as embezzlement, abuse of office, fraud and money laundering are connected to the purchase of the building. Several middlemen involved in the deal may have overcharged the Vatican, according to media reports.
The personnel changes come as the Vatican is preparing for a new evaluation by Moneyval, a monitoring body of the Council of Europe.
Moneyval Executive Secretary Matthias Kloth told Reuters last month after the police raids that the organization was “following developments closely”