The Express-Tribune said some polls closed before voters could cast their ballots, and some voters said they suspected irregularities in Sunday's vote as well.
The newspaper said about 5,000 security personnel were assigned to polling stations, which closed on time after a relatively uneventful day.
The turnout was considered low in comparison to the initial parliamentary vote held May 11.
That election resulted in a surprising win for the opposition PML-N party. A re-vote was ordered in some parts of Karachi that are strongholds of the ruling PTI party because some polling stations failed to open May 11.
Sunday's vote went on as scheduled despite the shooting death of a high-ranking official of the PML-N outside her Karachi home Saturday.