Prosecutors in the southern town of Trani alleged that five S&P officials had deliberately supplied markets with "tendentious and distorted" information about "the reliability of Italian credit and initiatives taken by the Italian government to restore and relaunch the economy".
The agency, the prosecutors added, helped "discourage the purchase of Italian public debt and thus drive down its value".
The S&P managers accused included former president Deven Sharma and other London-based managers.
Two Fitch managers, including ratings chief David Riley, were also accused of releasing information to the markets "that should have remained private" during trading hours, leading to price fluctuations.
Magistrates dropped allegations they had considered against Moody's. A judge will now rule on whether the managers should stand trial. Trani prosecutor Carlo Mario Capristo said on Monday that an audit court in the region of Lazio had also opened an inquiry and had estimated damages wrought by the agencies on the Italian treasury at €120bn (£96bn).
In a statement, S&P said: "These claims are entirely baseless and without any merit as our role is to publish independent opinions about creditworthiness according to our public and transparent methodologies, which we apply consistently around the world."
Fitch did not comment.
Investigators from Trani raided offices of the agencies in Milan in January after complaints from Italian consumers associations , complaints which had been turned down by magistrates in Milan and Rome.
Elio Lanutti, president of one of the consumer groups that took issue with the agencies, called them "an erratic danger to state sovereignty in the areas of economics and finance".
During their inquiry, prosecutors questioned Mario Draghi, the then president-designate of the European Central Bank, Italy's former prime minister, Romano Prodi, and Giulio Tremonti, who served as finance minister in Silvio Belusconi's government last year.
European policymakers have complained that while they have punished struggling national economies, ratings agencies missed the growing threat to the global economy from subprime mortgages, which triggered the economic crisis in 2008.
In a potentially precedent-setting ruling last week, a judge in Australia found S&P guilty of giving its highest rating to derivatives which then lost most of their value in the runup to the crisis.
Justice Jayne Jagot said S&P and ABN Ambro had deceived 12 Australian councils that bought the triple-A rated constant proportion debt obligation, notes created by the bank. After telling councils that the notes had less than a 1% chance of defaulting, the notes went on to default within six months, costing the councils A$16m (£10.4m). Jagot awarded the councils in New South Wales state A$30m for losses and damages. S&P said it would appeal, stating " We reject any suggestion our opinions were inappropriate."
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