"Wrong propaganda is being floated about intelligence agencies through newspapers. I want to tell them that the intelligence agencies are under the Pakistan government," Gilani said at an official function on the outskirts of Islamabad.
He contended that intelligence agencies, including the powerful ISI, function under the directives of the government.
"And without the government, they can't do anything that goes against national interests. If the ISI has done something, they had our backing and we are with them," he said.
Gilani's remarks came in the wake of a warning by Admiral Mike Mullen, America's top military official, that the ISI's long-standing ties with the Haqqani militant network are at the core of US''s strained and problematic relations with the Pakistan.
Secret documents leaked by WikiLeaks showed that the US military categorised the ISI along with al-Qaeda, Taliban, Lashkar-e-Taiba, Jaish-e-Mohammed and Harkat ul-Jihad al-Islami as terrorist or terrorist support groups.
The ISI was listed along with the terror groups in a document provided to officials who assessed terror suspects detained at Guantanamo Bay.
The revelation came at a time when ties between Pakistani and American spy agencies have hit a new low following the arrest in January of CIA contractor Raymond Davis for gunning down two Pakistani men in January.
Davis was pardoned and freed by a court after over two million dollars was paid as "blood money" under Islamic laws to the families of the dead men but ties between the ISI and the CIA are yet to be restored to an even keel.
Pakistan has also strongly opposed attacks by CIA-operated drones in its tribal belt, described by American officials as a haven for Taliban and al-Qaeda elements.