The bank, officially known as the Institute for Works of Religion (IOR in Italian), reportedly failed to provide a Milan affiliate of JP Morgan with details about payments into the account, in which €1.8 billion has been deposited in the last 18 months.
earlier this month the bank was listed by the U.S. State Department as being potentially vulnerable to money-laundering, Britain's Daily Telegraph reported.
JP Morgan had been requesting information on the source of deposits since 2010, after the IOR was accused of breaking money-laundering regulations by authorities in Rome, the Telegraph reported.
According to Italian financial daily Il Sole 24 Ore, JP Morgan Milan told the Vatican it would begin a phased closing of the account on March 16.
The paper added the account was a "sweeping facility" and was emptied every day with the funds transferred to an IOR account in Germany.
The latest incident follows a series of scandals involving the bank's checkered financial past.
In September 2010 Italian investigators froze €23 million in bank funds during a probe into possible money-laundering, placing its President Ettore Gotti Tedeschi under investigation.
But perhaps the most famous scandal involved then-IOR President Roberto Calvi and the collapse of Italy's largest private bank in 1982.
After the Banco Ambrosiano went bust, Calvi, also known as "God's Banker," was found hanged beneath London's Blackfriars Bridge.
Investigators were never able to determine if Calvi's death was a suicide or murder.