State comptroller Manuel Galindo said in a public address that he had launched a "fiscal audit" of the department headed by Attorney General Luisa Ortega, the highest official to break ranks with the government.
In an address to lawmakers later, Ortega complained that officials had burst into her offices like a "riot." She insisted she would cooperate with an audit as long as they showed "respect."
Ortega faces a court hearing Tuesday that could lead to her being put on trial over alleged misconduct.
Her supporters say it is punishment for her challenging the government and its allies, whom she has accused of breaching the constitution.
Her stand against President Nicolas Maduro has raised the prospect of a split in the government camp.
Maduro is under mounting pressure after three months of unrest that have left 89 people dead, according to prosecutors.
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