The Punjab election commissioner confirmed the development, saying the former premier's nomination papers were rejected due to "insufficient details of assets".
The by-polls on nine National Assembly seats vacated by the PTI will be held on September 25.
According to a notification issued by the ECP, the by-elections will be held for the constituencies of NA-22 Mardan, NA-24 Charsadda, NA-31 Peshawar, NA-45 Kurram, NA-108 Faisalabad, NA-118 Nankana Sahib, as well as NA-237, 239, and 246 of Karachi.
Earlier, the PTI announced on August 5 that Imran will contest by-elections across nine NA seats.
“Chairman Imran Khan will simultaneously contest from all nine National Assembly seats in the (upcoming) by-elections,” the party said in a tweet.