Chakraborty, a legislator from Berhampore in Murshidabad district who was last week permitted by the Congress high command to quit the ministry, said that his resignation letter has been sent to the chief minister.
"In my two-line letter I said that I tender my resignation from the ministry and request her to accept it," he said.
Chakraborty, a minister of state, had sent his resignation to Congress President Sonia Gandhi after Banerjee stripped him of the Parliamentary Affairs and Cottage and Small Scale Industries portfolios.
After he was given charge as minister of state for food processing, he had hit back dubbing the state government as dictatorial and also questioned the chief minister's performance.
Chakraborty, a close associate of senior party MP Adhir Ranjan Choudhary, had said he was not informed before the change of his portfolios.
WBPCC president Pradip Bhattacherjee said that his party had not yet decided on a replacement for Chakraborty.