Jain has resigned citing "personal reasons", a source said.
According to a submission by the Delhi Police in a court, Jain had disclosed that Aam Aadmi Party MLAs Prakash Jarwal and Amanatullah Khan had surrounded and assaulted chief secretary Anshu Prakash at Chief Minister Kejriwal's residence late at night on February 19.
Jain, however, had initially said he had not seen anything as he was in the washroom when the incident is alleged to have taken place.
"Jain has resigned from the post of advisor to the chief minister citing personal reasons and family commitment," the source said.
He had been absent from the CMO since the incident and had gone on a week-long medical leave, government sources said.
Jain was among those present at the meeting at the CM's residence when Prakash was allegedly assaulted by the AAP MLAs in the presence of Kejriwal and his deputy Manish Sisodia.
He was appointed to the post in September last year, days after he had retired as the CEO of the Delhi Urban Shelter Improvement Board (DUSIB). The board is chaired by Kejriwal.
Since the alleged attack on the chief secretary, IAS and DANICS officers have not been attending meetings with AAP ministers, and only maintaining written communications with them.
There are around 70 IAS and 450 DANICS officers working with the Delhi government.
A joint forum of the Delhi government employees has demanded action against Kejriwal and Sisodia in connection with the case. They have also been observing a five-minute silence at work every day.
Since the AAP government was formed, the Delhi government and the bureaucracy have been at loggerheads on a range of issues.
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