Federal Judge Julian Ercolini approved charges of illicit association and fraudulent administration against Fernandez, and two former aides: ex-Planning Minister Julio de Vido and former Public Works Secretary Jose Lopez.
Also named was businessman Lazaro Baez, whose Austral Construcciones company allegedly benefited from irregular contracts.
The judge's order froze the equivalent of up to $633 million of each defendant's assets, though it was not clear they have that much.
The ruling published by official Center of Judicial Information said the defendants are accused of associating to illegally take public fund meant for public works between May 2003 and December 2015.
Fernandez made no immediate comment on the charge, but she has repeatedly denied wrongdoing.
Since leaving office in December 2015, Fernandez has alleged that she is the victim of persecution by her conservative successor, Mauricio Macri.
In May, a judge indicted Fernandez on charges of manipulating currency exchange futures markets, allegedly causing economic damage to the government.
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