The report by Vatican financial investigators zeroes in on the activity of Giampietro Nattino, chairman of Banca Finnat Euroamerica S.p.A, a family-run private Italian bank.
Vatican investigators suspect Nattino used the APSA accounts for personal trades on the Italian stock market, the report says, adding that the balance of more than 2 million euros was moved to Switzerland when the accounts were closed days before the Vatican introduced stricter new laws against money laundering that put money transfers under more scrutiny.
From May 22, 2000 to March 29, 2011 Nattino, who has served on the board of many Italian firms and volunteered as an usher in the papal palace, was the owner of APSA "Portfolio 339", which consisted of four separate accounts, the report says.
The report speaks of the "dubious origin and dubious final destination of the funds in the closing of portfolio 339" and asks why Nattino was allowed to have accounts at APSA in the first place in apparent violation of department regulations.
Those regulations, which are published on the Vatican's website and mentioned in the internal report, say the department can carry out financial transactions for third parties only on an "exceptional basis" and only with prior permission of the cardinal in charge.
Financial investigators gave their findings to the Vatican's Promoter of Justice, or chief prosecutor, Gian Piero Milano, a senior Vatican source said, adding that Milano had opened his own investigation.
The investigators asked the prosecutor to look into possible money laundering, insider trading and market manipulation related to Nattino's accounts at the conclusion of their report, which includes some 30 charts and graphs detailing stock holdings and transactions and bank transfers.
Vatican investigators suspect that on one occasion when his bank handled a stock placement, the APSA accounts were used to buy shares before they were allocated to other investors, according to the document.
The investigators also asked the prosecutor to look into "potential co-responsibility" by APSA staff in execution of the activity in the accounts and if the procedures followed "rules and internal practices" at the department.
Nattino's daughter Paola, who acts as company spokeswoman, declined to comment about Portfolio 339 and suspicions of irregularities connected to the accounts, saying in an email to Reuters that "it is our custom not to issue statements".
Milano's office did not return phone calls about the case. It has said in the past that it does not comment on investigations.