Jarwal was arrested by Delhi police on late Tuesday night.
Delhi Police spokesman Dependra Pathak said Chief Minister Arvind Kejriwal's adviser VK Jain was also questioned for three hours on the complaint by Mr Prakash.
"One AAP MLA Prakash Jharwal has been arrested by Delhi Police on a frivolous complaint by IAS", AAP chief Spokesperson Saurabh Bharadwaj said in a tweet.
The BJP protest came in the wake of the alleged assault on Prakash during a meeting at the Chief Minister's residence on Monday night.
Reacting sharply to the alleged man-handling of Delhi Chief Secretary, DPCC chief Ajay Maken said that strict legal against concerned persons for this such behaviour.He also said that the capital went through administrative paralysis alleging that officials were not able to work properly under this government in Delhi.
Baijal submitted a report on the incident regarding Prakash to the Home ministry on Wednesday.
On Twitter, the party claimed: "About 2.5 lakh families deprived of rations last month due to faulty implementation of Aadhaar". AAP MLAs are accused of allegedly assaulting the chief secretary.
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There was chaos at the Delhi Secretariat, as employees protested outside the Chief Minister's Office.
"He even used bad language against some MLAs and left without answering any questions", the spokesman said. Addressing the 71 Raising Day Parade of Delhi Police here today, he directed the Delhi Police top brass to update the crime control strategy.
Reports quoted DCP Madhur Verma as saying that Amanatullah Khan was detained at around 11.30 am in connection with the investigation of case regarding the assault on the Chief Secretary. MLAs were under tremendous pressure from public.
He alleged that the Central Government uses CBI as a tool against the AAP leaders by making it to raid the offices and homes of AAP leaders.
"The said assault and manhandling of a senior bureaucrat on February 19, 2018 by sitting MLAs are highly disturbing, outrageous, shocking and highly deplorable", the association said. The fierce political rivalry between the two parties in power at the Centre and the state has long descended into bitter public acrimony, which perhaps makes climbing down over any issue hard. The civil servants should be allowed to work with dignity and without fear.
"The way Kejriwal government is behaving, it is clear that the entire administration has been stalled".