Governor Ebad's Muttahida Quami Movement (MQM) had protested against the operation and alleged that nearly 100 of its activists have been arrested, Xinhua reported.
There was no official word on governor's resignation. However, sources in the Governor's House said that Ebad had faxed his resignation to the presidency.
The rumours of the resignation gripped the country after the sudden departure of Ebad to Dubai late Friday.
It was reported that Ebad would stay in Dubai for a couple of days and later proceed to London to meet the MQM's self-exiled chief Altaf Hussain.
Ebad has served as governor for 11 years and has been loyal to the MQM, the powerful group of the ethnic Urdu-speaking people in Karachi and urban areas of Sindh.
The Pakistan government, with consultation of the provincial government, has given a go ahead for operation against terror groups, kidnappers, extortionists and criminal gangs as violence had claimed many lives and affected business activities.
The operation caused tension between the MQM and the government after the police arrested a former lawmaker of the group in connection with the killing of two policemen.
The MQM said its supporters are the main target of the operation launched by the paramilitary troops with the support of the police.
--IANS (Posted on 14-09-2013)