"Jain has resigned from the post of advisor to the Delhi chief minister citing personal reasons and family commitment," one of the sources told PTI.
He has submitted his resignation letter to the Chief Minister's Office (CMO) and sent a copy to the lieutenant governor, the source added.
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Jain had not been coming to the CMO since the incident and had gone on a week-long medical leave, the sources said.
Prakash was allegedly assaulted by AAP MLAs during a meeting at the chief minister's residence in the evening of February 19.
The Delhi Police had last week told a court that during interrogation, Jain disclosed that AAP MLAs Prakash Jarwal and Amanatullah Khan surrounded the chief secretary and saw them assaulting him at Kejriwal's residence.
However, Jain had earlier said that he did not see anything as he had gone to the washroom at the time of the incident.
The alleged assault on Prakash took place in the presence of Kejriwal and his deputy Manish Sisodia.
In solidarity with Prakash, IAS and Delhi, Andaman and Nicobar Islands Civil Services (DCS) officers have not been attending meetings with AAP ministers, and only maintaining written communication with them.
The joint forum of the Delhi government employees has demanded action against Kejriwal and Sisodia in connection with the case.
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