Chief Election Commissioner Sardar Raza Khan, heading a five-member bench, issued the warrant against 64-year-old Khan after he failed to appear before it or offer apology in the case.
Khans lawyer Babar Awan urged the EC to delay the proceedings till the Islamabad High Court decides the issue of the election commission's jurisdiction in contempt case.
In Pakistan, election commission can issue arrest warrants.
Meanwhile, Khan's Pakistan Tehreek-e-Insaf party said it would challenge the decision in the High Court.
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However, his party approached the Islamabad High Court which, on September 20, suspended the bailable arrest warrants.
In the previous hearing, Khan, in his reply submitted through his lawyer Babar Awan, had stated that he confirmed the apology tendered by his previous counsel regarding the "contemptuous" remarks, adding that the contempt of court matter is a "closed transaction belonging to the past".
His counsel then requested the ECP to withdraw a show- cause notice issued on September 24.
Akbar Babar, the petitioner who had filed the foreign funding case against the PTI leadership, had informed the ECP that Khan had accused it of being biased in the foreign funding case following which his counsel tendered an apology with the commission.
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