A letter from TMC chief Banerjee replacing Roy, who has been under CBI scanner in the Saradha chit fund scam, was sent to Rajya Sabha Chairman Hamid Ansari.
Sources confirmed that a letter in this regard has been received at the Chairman's office.
Roy, who was once considered to be the closest to the West Bengal Chief Minister, has fallen out of favour with her ever since his questioning at the hands of the CBI in the Saradha chit fund scam.
The sources said no decision has been taken on who will be the new chief whip of the party.
A number of changes have recently been initiated in the Trinamool Congress, which includes Roy's removal as general secretary and inclusion of O'Brien as Secretary.