Former European Cup finalists Sampdoria, now playing in Serie B, were also named along with 52 players, the Italian federation (FIGC) said in a statement.
They have been referred to the FIGC's disciplinary committee following investigations by magistrates in the northern city of Cremona which began in December.
Italian media reported that there is likely to be a huge sports trial in the next few months.
The FIGC listed 33 matches, nearly all in Serie B but including two in the Coppa Italia, as being under suspicion of manipulation over the last few seasons.
Atalanta, Novara and Siena were all playing in Serie B at the time of the alleged match manipulation.
Atalanta began this season with minus six points after they were among 17 clubs to have points deducted last August over match-fixing.
Former Atalanta captain Cristiano Doni, banned for three-and-a-half years in the same verdict and arrested last December, was among the 52 players listed in the latest investigation, the FIGC said.
In April, former Bari defender Andrea Masiello was arrested in connection with alleged match-fixing in Serie A last season.
Eight of Masiello's team mates from Bari last season were also being investigated by police over the possible manipulation of matches.
Bari's chief prosecutor Antonio Laudati said investigations suggested a total of five matches had been manipulated during the 2010/11 season and 2009/10.
Juventus, who won this season's Serie A title on Sunday, were demoted to Serie B in 2006 because of match-fixing and were stripped of their 2005 and 2006 Serie A titles.
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