The civil proceeding is separate from the criminal case against the prominent Wall Street figure, who is accused of bilking $50 billion from investors in what may be the largest Ponzi scheme in history.
Federal prosecutors have asked a judge to revoke the bail of Madoff, who has been confined to his Manhattan penthouse.
The agreement with the SEC says the agency's civil fraud allegations cannot be contested by Madoff and that possible civil fines and restitution will be decided "at a later time."
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