The Bank of Italy defended its role in supervising Italian banks, denying knowledge of the trades.
Its investments give the Bank of Italy a substantial indirect stake in the banking business.
Officials at the Bank of Italy suspected that Mr Berlusconi was behind the Swiss companies.
Investigations began after an inspection by the Bank of Italy two years ago uncovered anomalies at Sofige.
"The Bank of Italy is a supervisor but is not the police of the banks, " he added.
The Bank of Italy has access to lots of market-sensitive information, and it also sets interest rates.
The bank of Italy's protectionism can only do damage to Italian banks, says one Italian bank boss.
Consider the fate of a recent proposal by the respected governor of the Bank of Italy, Mario Draghi.
Mr Monti expressed "full confidence" in the Bank of Italy under Ignazio Visco and previously under Mr Draghi.
The Bank of Italy, which last examined Banca di Roma in 1995, declines to comment on individual banks.
The Bank of Italy's deputy director in Palermo helped the magistrates dig further.
The Bank of Italy refuses to comment on its equity investments and will not say how they are managed.
One indicator is that the Bank of Italy's appointments in the mezzogiorno are for only two to three years.
The Bank of Italy reckons that inefficiency in civil justice costs Italy as much as 1% of annual GDP.
The Bank of Italy also parks part of its statutory reserves in equities.
The magistrates asked the Bank of Italy to help the anti-Mafia division investigate.
The Bank of Italy and the employers' association, Confindustria, have plumped for 4.9%.
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It is said that two European central banks were worried enough to have requested information from the Bank of Italy.
This provoked the first of a series of clashes between Mr Tremonti and Antonio Fazio, governor of the Bank of Italy.
The "wise men" included a former head of the constitutional court, a member of the Bank of Italy's board and senior politicians.
Speaking from Paris before news of the violence, the chief of the Bank of Italy, Mario Draghi, expressed sympathy with the protesters.
The Bank of Italy said this week that state revenues fell by more than 3% in the first five months of 2009.
This was his final appearance as ECB president before handing over to Mario Draghi, the head of the Bank of Italy, in November.
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He can only be dismissed by the Bank of Italy's 13-man Superior Council, which is composed of senior businessmen, academics, lawyers and economists.
It will take over the supervision of debt issuance from the Bank of Italy, and it will get some of the bank's staff and property.
The Bank of Italy has encouraged such consolidation, but it has tried to arrange the mergers itself, earning a reputation as Italy's biggest deal maker.
Two people close to the Bank of Italy said Mr Draghi as governor had ordered intense scrutiny of Monte dei Paschi, including the 2010 visit.
There is clearly a problem, but neither the Bank of Italy, the country's central bank, nor the Italian banking association can put figures on it.
Currently the governor of the Bank of Italy, Mr Draghi is due to replace Jean-Claude Trichet in the top job at the ECB on 1 November.
The Bank of Italy's outgoing governor, Mario Draghi, spelt things out recently in a hard-hitting farewell speech (before taking the reins at the European Central Bank).
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