APP said the Okhla MLA was "spreading falsehood" and there was no mention of the incident in the party manifesto.
"Asif has tried to spread a lot of falsehood today. Without reading the AAP manifesto, he has given statements that it promises a probe into this encounter. There is no such mention in the AAP manifesto," said a statement issued by the party on late evening today.
Khan today barged into the press conference at Delhi Secretariat and started shouting slogans against AAP after Arvind Kejriwal, in reply to a question, said that Delhi Government would not form an SIT to investigate the encounter.
The party said that the Congress was in power at Centre and in NCT when the incident took place.
"This encounter had taken place on September 19, 2008 when there were Congress governments in Delhi as well as at the Centre," the statement said.
The party questioned the reason of the Okhla MLA joining the Congress ahead of Assembly polls last year, if he had doubts over the encounter.
"Mr Asif needs to answer the question as to why he joined the Congress in August 2013 after having won the 2008 Assembly polls on the RJD ticket. Despite the fact that Congress governments of Delhi and even the Centre had termed the encounter as genuine in the High Court and the Supreme Court," the statement said.
The statement further said that when the encounter took place, AAP had not come into existence.
"The AAP had not come into existence till then, but it was noted lawyer and human rights activist, Prashant Bhushan (now a national executive member of the AAP) who had filed a petition in the Delhi High Court seeking an independent investigation into this encounter."
The HC asked the National Human Rights Commission (NHRC) to look into the matter. The NHRC accepted the probe report of the Delhi Police Crime Branch. This was again challenged by Bhushan in the Supreme Court," the statement added.
A three-judge bench of the Supreme Court, headed by the then Chief Justice of India KG Balakrishnan dismissed the petition seeking an independent/judicial inquiry into the encounter. The apex Court ruled that no further probes were required in this matter.