Prakash later met lieutenant governor Anil Baijal and complained to him about the alleged incident.
The BJP on Tuesday demanded Arvind Kejriwal's resignation over alleged manhandling of the Delhi chief secretary by a few ruling AAP MLAs, while the Congress termed the incident an "administrative and constitutional crisis", and sought an apology from the chief minister.
The chief minister's office, however, has dismissed the accusation of chief secretary Anshu Prakash being assaulted on Monday night as "bizarre and baseless".
Describing the alleged incident in presence of Arvind Kejriwal and his deputy Manish Sisodia at the former's residence "an act of Urban Naxalism", Delhi BJP president Manoj Tiwari sought Kejriwal's resignation, a high-level inquiry against him and suspension of the legislators concerned.
"ArvindKejriwal and his Goon MLAs misbehaved and threatened the Chief secretary of NCT Delhi Government last night... Another shameful act of @AamAadmiParty Goons... An act of Urban Naxalism... #UrbanNaxaliteKejriwal must Resign (sic)," he tweeted.
Echoing his sentiments, a senior BJP leader claimed that in total, nine AAP MLAs were present at the chief minister's residence when Prakash was assaulted.
"They represent the people of Delhi but are nothing short of Urban Naxalites. How utterly disgusting behaviour!," he said.
Delhi Congress president Ajay Maken launched a scathing attack on the AAP government, accusing it of being a complete failure and demanded that Chief Minister Kejriwal apologises for this "hooliganism".
Kejriwal should apologise for this hooliganism which took place before him-AAP Govt is unable to deliver-Beating of Chief Secretary by MLAs in front of CM is another low & is aimed to divert attention from Govt failures! AAP does not know Governance and has failed miserably (sic)," Maken said in a tweet.
Senior Congress leader J P Agarwal sought L-G's intervention and said that an all party meeting should be called in this regard.
"We have run Delhi government for 15 years and never has there been such a problem. One should not stoop to such level," he said.
Meanwhile, the AAP has alleged its leaders Ashish Khetan and Imran Hussein were heckled and their party volunteers thrashed by a mob inside the Delhi secretariat.
"Ashish Khetan and Imran Hussain heckled in Secretariat, volunteers thrashed by motivated elements showing up as employees. Delhi police says can't help," tweeted the party's official handle.
AAP leader Ashish Khetan has alleged there was an 'unruly and aggresive mob' at the secretariat who 'ran towards me shouting pro-BJP slogans'. He has accused the Delhi police of not intervening into the alleged incident.
(With PTI inputs)