The chief secretary had approached the police on Tuesday, alleging that he was assaulted by a group of MLAs during a midnight meeting at Kerjriwal's residence.
Jain had first told the police the Chief Secretary was not assaulted in his presence.
The MLA, in his compliant, alleged that the chief secretary passed casteist comments against him during the meeting at Chief Minister Arvind Kejriwal's residence.
Senior AAP leaders Ashutosh and Sanjay Singh claimed that this was a ploy to destabilise the party's government in Delhi.
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According to the statement, Jain also saw that the Chief Secretary's spectacles had fallen to the ground and the Chief Secretary picked them up and left the room.
The officer said that the statement under section 164 has also been submitted to the court. Jain, a witness in the case, was questioned for hours by the Delhi Police on Wednesday.
Meanwhile, the court on Thursday sent the two AAP MLAs Amanatullah Khan and Prakash Jarwal to Tihar Jail. Metropolitan Magistrate Shefali Barnala Tandon extended the judicial custody of the two MLAs by another 14 days while deciding to hear their bail plea on Friday afternoon.
BJP workers of New Delhi Assembly area, which is represented by the Mr Kejriwal, held a prayer meeting outside the famous Birla Mandir which was led by New Delhi District BJP president Anil Sharma as the Chief Minister has no public contact office in his constituency.
"This protest will continue on all working days at 1:30 pm in all the Delhi government offices, Jal board, other affiliated offices till the political executive takes tangible steps to ensure safety and dignity of all government employees", Manisha Saxena, secretary of IAS Association, said.