The court, which is dominated by government loyalists, said Luisa Ortega Díaz had committed serious errors.
Ms Ortega, once a staunch government ally, broke ranks in March when she said an attempt by the Supreme Court to strip the opposition-controlled Congress of its powers was unlawful.
Critics believe President Nicolás Maduro is trying to push Ms Ortega out.
She faces a hearing on 4 July - some analysts say she may eventually be put on trial. The move comes amid growing political turmoil in Venezuela.
According to reports, the accusations against her refer to the appointment of judges.
The Supreme Court recently transferred Ms Ortega's powers of investigation to the national  ombudsman.
On Wednesday, she strongly criticised President Maduro following an incident in which a stolen police helicopter flew over government buildings in the capital, Caracas, dropping grenades and firing shots.
Mr Maduro called it a "terrorist attack" but Ms Ortega said Venezuela was suffering from "state terrorism" due to the harsh response by authorities to anti-government protests.
The suspected pilot, a rogue elite police officer identifying himself as Oscar Pérez, posted Instagram videos admitting the attack and calling on Venezuelans to rise up against the government.
Venezuelan security forces later said they had found the helicopter, near the north coast in the state of Vargas. There was no sign of the pilot.
Andrew Rosati, a Caracas-based journalist for news website Bloomberg, said some people doubted the government's version of events.
"I spoke to people today on the streets and some are absolutely mystified by the whole affair," he told the BBC's Newsday programme.
"This idea that a helicopter almost vanished into the air, flew off into the sunset. Many think this whole thing is staged by the government."
Opposition politician and parliamentary Speaker Julio Borges also raised the possibility that the incident was a hoax but said more information was needed.
"Whatever it is, it is very serious," he said. "It all points to one conclusion: that the situation in Venezuela is unsustainable."
There have been almost daily anti-government protests in Venezuela for more than two months as the country's economic and political crisis worsens.
Venezuela's Supreme Court has banned the attorney general from leaving the country and frozen all of her assets.