The Central Intelligence Agency 's relations with the ISI had come under strain before the arrest of double murder-accused US diplomat Raymond Davis, as ISI officials expressed their anger over US complaints that the agency had not done enough to clamp down on Taliban militants in its tribal region bordering Afghanistan.
As the relationship deteriorated, the ISI began holding up visas for US government employees in the early part of 2010, The Wall Street Journal reported.
The backlog built up as Washington launched a series of bilateral engagements with Zardari's government aimed at improving relations with Pakistan, it added.
To get around the delays, Pakistan Prime Minister Yousaf Raza Gilani passed a directive in July, allowing the embassy in Washington to issue visas without any security clearance from the ISI.
The ISI has been angered by "the desire of the Obama administration to go through the civilian government," the Pakistani government official said.
Despite its democratically elected government, Pakistan's military, which has ruled the country for more than half of Pakistan's 63-year history, still plays a key role in many areas of policy, the report said.
The ISI officer said Davis was apparently part of a team looking into the actions of Lashkar-e-Taiba, a violent Islamist group that has traditionally focused on attacking India but is seen by the US as a threat in Afghanistan.
Pakistan's spy agency blamed the civilian government for allowing US intelligence operatives to enter the country secretly, sparking an internal feud over the double murder by the detained CIA contractor, and complicating US policy in the region.
The ISI says the Zardari government has pushed visa policies that it claims have made it easier for CIA employees and contractors, including Davis, to operate secretly in the country.
However, senior Zardari administration officials deny this, saying that the ISI is using the shootings to weaken the democratically elected government. (ANI)
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