The Bank of Italy told commercial banks to stop processing electronic transactions until the Vatican had fully implemented European Union measures to prevent money laundering.
The Bank of Italy said the central bank in December denied a permit for Deutsche Bank Italy, the Vatican's previous provider of electronic payment services.
This was because the Holy See was seen as lacking anti-money laundering controls and oversight.
Deutsche Bank's Italian operation needs approval from the Bank of Italy to provide the credit card service under Italian banking regulations.
In a report by Moneyval last year, a Council of Europe-backed committee, found serious failings in the Vatican bank and urged it to strengthen measures to prevent money laundering and increase transparency.
The Vatican has struggled to shake off a reputation for a lack of financial transparency that dates back to 1982, when Roberto Calvi, an Italian known as "God's banker" because of his links to the Vatican, was found hanged under London's Blackfriars Bridge.
A Vatican statement said only that its agreement with a bank that previously supported point-of-sale payments had expired.
It said talks were under way with other service providers and the interruption to electronic payments was expected to be "of brief duration".
No further comment was immediately available from the Vatican.
Deutsche Bank and the Bank of Italy also did not respond to requests for a statement on the matter.
The sale of postage stamps, memorabilia and admission tickets to the Vatican Museums, home to art treasures including Michelangelo's Sistine Chapel, constitutes the Holy See's main source of income apart from donations and investments.
In 2011, 5m museum visitors brought in €91.3m according to the city state's annual financial report, in which it posted its worst budget deficit in more than a decade.
The report did not state what percentage income came through card payments.
A notice posted on the Vatican Museum's website said it was not possible to take electronic payments within the Vatican from 1 January "for reasons beyond the control of the Directorate of the Museums".