Town Supervisor William McGintee's administration is under both state and local investigation for misusing town preservation funds.
A deputy to the town clerk says the Democratic official filed his resignation letter Monday morning.
McGintee's top budget aide, Ted Hults, was arrested in June. Charges against Hults include defrauding the government, official misconduct and fraudulent practices regarding stocks, bonds and other securities.
A spokesman for Suffolk District Attorney Thomas Spota had no comment because there is an ongoing grand jury investigation of the Town of East Hampton.