"We have received complaints about rigging from several constituencies in Karachi and Hyderabad and we will be investigating them," Chief Election Commissioner Fakhruddin G Ebrahim said.
He said that re-polling will take place in more than 40 polling stations in NA-250 constituency in Karachi.
It was alleged that at many stations there was no staff and ballot boxes were absent or snatched by miscreants.
The EC has ordered that polling taking place in these constituencies be stopped immediately.
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The extension was allowed after complaints that voting at many polling stations started after a delay of three to four hours while at a polling station Karachi (NA-250), voting didn't start until 5.00 P.M.
The Jamaat-e-Islaami and Sunni Tehreek announced they were boycotting the elections in Karachi after levelling allegations of rigging and harassement against the MQM which in turn has boycotted elections in NA-248 that includes Lyari and two provincial constituencies.
The PTI and JI said that Karachi was being "held hostage" yet again. Both PML-N and PTI said they would not accept election results in Karachi.
The parties have lashed out and blamed the EC for the faux pax in some constituencies in Karachi and Hyderabad.