The ministry is also looking into the working relations between bureaucrats and the political executive of the Delhi government.
"There are certain issues in the case which are being investigated and inquired into by the Delhi Police," the official said.
Referring to the statement of Home Minister Rajnath Singh, the official said "justice will be done" to all concerned.
Without divulging the contents of the report, the official said one of the accused MLA has been arrested, while another has surrendered before the police.
Yesterday, a delegation of IAS, DANICS and subordinate services of Delhi government met the home minister, who said civil servants should be allowed to work with dignity and without fear.
The delegation met the home minister after Delhi Chief Secretary Anshu Prakash was allegedly manhandled by a few AAP MLAs at Chief Minister Arvind Kejriwal's residence, which the team of bureaucrats termed as a "pre-planned and pre-meditated" attack.
"I am deeply pained by the happenings involving the chief secretary of the Delhi government. The civil servants should be allowed to work with dignity and without fear. Justice will be done," Singh had said.
The home ministry yesterday sought a report on the incident from the Lieutenant Governor of Delhi.
The incident occurred Monday night in presence of Kejriwal and Deputy Chief Minister Manish Sisodia , a senior Delhi government official alleged.
Prakash was called by Kejriwal regarding the issue of advertisements, which were not being released, the official said.
However, the Aam Aadmi Party (AAP) claimed he had been called for a discussion on ration distribution.
"The allegation of assault is totally bizarre and baseless," a senior official of the chief minister's office said.