In a communication, the ministry asked the LG to submit a detailed report on the alleged attack on bureaucrat Anshu Prakash at the residence of Delhi Chief Minister Arvind Kejriwal on Monday night.
The home minister would also meet a delegation of IAS officers of the Delhi government, a ministry official said.
"The home ministry is aware of the development and closely monitoring the situation," the official said.
In a tweet, Mr Rajnath Singh said he was "pained by the happenings" and that civil servants should be allowed to work with dignity and without fear.
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.- Rajnath Singh (@rajnathsingh) February 20, 2018
Chief Secretary Prakash was manhandled by a few AAP MLAs at Mr Kejriwal's residence, an IAS officer alleged on Tuesday.
"There was a heated exchange at the meeting last night. During the argument, two or three AAP MLAs manhandled him... The CS's spectacles also got broken," the senior IAS officer, who did not wish to be named, claimed.
The chief minister's office dismissed the accusation as "bizarre and baseless".
"The allegation of assault is totally bizarre and baseless," a senior official in the chief minister's office said.