Siddique told reporters at Kozhikode that he had sent his resignation letter to KPCC President V M Sudheeran and informed Chief Minister Oommen Chandy of the matter.
Rejecting the charges, he said "I am resigning on moral grounds in the wake of the complaint. I want to keep away from the post till I am absolved of the charges levelled."
Sudheeran said he had received Siddique's resignation and it would be accepted.
In a Facebook post, Siddique had said that a conspiracy was behind the allegations to politically destroy him.
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Siddique's former wife, a cancer patient, had alleged she and her two children were intimidated and assaulted when she went to a hospital at Kozhikode for a check-up recently.
Siddique, a former state Youth congress president and a confidant of Chandy, had unsuccessfully contested from Kasargod Lok Sabha seat in the Lok Sabha elections last year.