His lawyers filed a petition Friday questioning the move by government prosecutors in indicting him without giving him a chance to reply to the charges first.
They also asked the Supreme Court to order the anti-graft court, the Sandiganbayan, to throw the cases back to Ombudsman Aniano Desierto, the chief government anti-graft investigator and prosecutor.
The request could delay a decision by the Sandiganbayan on whether to order the arrest of Estrada.
Estrada was indicted Wednesday on accusations he pocketed $82 million in kickbacks and payoffs during 31 months in office.
The charges were filed by Desierto a day after the Supreme Court unanimously rejected Estrada's appeal to reverse the tribunal's ruling that stripped him of immunity.
The ruling reaffirmed the legitimacy of the presidency of Gloria Macapagal Arroyo, who was Estrada's vice president.
Estrada, who was forced to step down Jan. 20 amid mass protests sparked by corruption allegations.
But Estrada never signed a resignation letter and later asked the Supreme Court to declare Arroyo only "acting president." The Supreme Court ruled he effectively resigned when he left the palace.
Among the charges leveled against Estrada were plunder a non-bailable offense that could lead to Estrada's arrest. Plunder illegally accumulating more than $1 million while in office is a capital crime, but it is considered doubtful Estrada would get the death penalty.
Desierto also charged the once-popular film star with violation of the anti-graft law, misuse of public funds, perjury, illegal use of an alias, illegal gambling and violation of the law on ethical standards.
Desierto said the $82 million allegedly "plundered" by Estrada include more than $60 million in a secret bank account under an alias, $10.9 million in payoffs from illegal gambling, $2.6 million in kickbacks from a tobacco excise tax and $3.78 million in commissions from a stock sale using state pension funds.
Estrada reported $700,000 in net worth two years ago.
Estrada said Wednesday the charges are "fabricated" and he will "exhaust all legal remedies" though he doubts a fair trial is possible.
"I'm already convicted here through publicity so how do you expect to get a fair trial under this administration," Estrada told a reporter in an interview at his Manila home Wednesday.
Estrada lawyer Raymund Fortun said the ousted leader's right to due process was violated because he was deprived the right to participate in the preliminary investigation of the charges.
"We were actually very much ready to file the counter-affidavits but obviously there was never any opportunity given to the respondent to reply," Fortun said.
Fortun sai Estrada did not respond to complaints of corruption while the Supreme Court deliberated on his first appeal because that could be misinterpreted as a waiver of the former president's immunity.
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