Karamollaoğlu said in a television show on Turkish channel Halk TV on Tuesday that he found he had been blacklisted when he went to renew his passport following the June 24 general elections last year.
"My passport was cancelled by adding the word 'terror' to the beginning of my name," Karamollaoğlu said.
He was allowed to get his new passport 15 days later, but nevertheless the authorities blacklisting a political party's leader was "scandal," Karamollaoğlu said.
Tens of thousands of Turkish citizens had their passports invalidated via government decrees under the emergency rule declared following a coup attempt in 2016.
The interior ministry in March declared that Turkish passports belonging to 57,191 people which were cancelled over suspected criminal activity have been reinstated.
Following the Islamist leader's statements, journalist Kemal Göktaş on Twitter said Karamollaoğlu should have informed the public about this incident earlier, adding that the incident was "a serious violation of rights", and not only a personal issue.