The cricketer-turned-politician had accused the ECP of being biased in the foreign-funding case following which his counsel had tendered an apology with the commission.
The PTI is set to challenge the warrants in the Islamabad High Court.
"We have chose to challenge the ECP order today because it is illegal and the commission has no jurisdiction to issue any arrest warrants for a political leader", Khan's spokesman Naeemul Haq told Anadolu Agency.
Imran Khan was summoned by the ECP for the hearing of a case filed on October 26, against the former Pakistan cricket captain, by one PTI's founding members, Akbar S Babar. Earlier, a bailable arrest warrant was issued by the ECP on September 14, after Khan failed to appear for the hearing on the case.
The petition accuses the PTI leader of not declaring his assets to Election Commission of Pakistan.
They said that the decision to arrest Imran Khan is based on discrimination, adding that the ECP is not a competent authority to issue such warrant and due to its biased attitude it can not hold fair elections either.
Khan is also facing a case against him in the Supreme Court where the ruling Pakistan Muslim League-Nawaz (PML-N)'s petition is seeking his disqualification. And after Khan's repeated failures to address the commission, ECP issued a formal show-cause notice, asking him to reply by August 23.