Asim Hussain, a former federal minister and the Chairman of the provincial Higher Education Commission (HEC), was picked up from his office and taken to an unknown location by the plain-clothed intelligence officials.
Top Pakistan Peoples Party (PPP) leaders, including the opposition leader in the National Assembly, criticised the manner in which Hussain was taken to an unknown location.
"This is not the way," Opposition leader Syed Khursheed Shah said.
HEC sources told Dawn that some 15 plain-clothed personnel arrived at the HEC office in three to four vehicles around noon and took away Hussain.
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The men entered the boardroom where Hussain was chairing a meeting to appoint vice chancellors and they asked the attendees of the meeting to switch off their cellphones, following which the Sindh HEC chairman was whisked away to an undisclosed location.
Hussain's detention is significant since he is said to be a close confidante of Zardari the co-chairperson of the PPP.
There have been strong rumours that the government and military have agreed to crackdown against parties and high- profile politicians in Karachi in connection with cases against them of corruption and misuse of power.
Karachi's single-largest party, the Muttahida Qaumi Movement (MQM), claims hundreds of its supporters have been arrested or targeted by paramilitary forces in recent months on accusations of political corruption and violence.