The Higher Education Commission (HEC) executive director, Prof Dr Sohail Naqvi, was removed from the post on Thursday.
Qamar Zaman, the secretary ministry of education and training, was given the additional charge, it has been learnt.
About 70 contractual employees of the HEC held a protest and warned that they would go on a strike if Dr Naqvi was not reinstated. On the other hand, another group of HEC employees welcomed the appointment of the new executive director.
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