The FIR was lodged at Parliament Street Police Station last night against the AAP protesters and it included names of Ashutosh and Ilmi who were at the site of clashes yesterday.
Police had initially detained 33 people out of which 14 were arrested late last night while others were allowed to go.
28 people, including 13 AAP activists and 10 BJP supporters, were injured in the clashes, police said.
Ilmi accused the Delhi Police of targeting the AAP and wondered why no action was being taken against BJP activists.
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"Yesterday, we got to see the discrimination of Delhi Police, which joined BJP to disperse AAP supporters staging silent protest. Police could not see bricks, stones and chairs being thrown from the inside of BJP Headquarter...They could only see people much later retaliating. Police were protecting BJP supporters," Ilmi charged.
Ashutosh also accused Delhi police of bias against AAP workers.
"AAP supporters were injured in the clash. BJP leaders beat up our supporters. Delhi Police takes action when flower pots at BJP office were damaged but they didn't take action when our supporters were injured," he charged.
Police said they have got the entire sequence of events videographed. Senior officials said more arrests are likely in the case.
AAP workers had yesterday fought pitched battles with BJP activists outside the saffron party headquarters here hours after party leader Arvind Kejriwal was detained briefly in Gujarat.