The move comes after Khan repeatedly failed to appear before the five-member bench of the electoral commission.
PTI leader Babar Awan declared the ECP decision unconstitutional and said the party will file a petition in Islamabad High Court (IHC) against the verdict.
The ECP further accused him of underestimating the authority of the commission and "bringing it into disrepute and disrespect and to interfere with, obstruct, interrupt and prejudice the process of law and the due course of proceedings, and scandalising the commission".
In a written response that accompanied the documents, Imran said that he had mentioned the transfer of the money from his account to Jemima's in financial documents submitted before the Election Commission of Pakistan in 2003.
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The petitioner alleged that Khan received almost $3 million in foreign funds that were collected through two offshore companies.
The PTI rejected the electoral body's order to arrest their party chief, terming the move "illegal".
In Pakistan, election commission can issue arrest warrants.
He came down hard on opponents and said that only Nawaz Sharif was held accountable while there were over 400 people named in the Panama Papers list.