Gates, who is visiting Islamabad after discussing the South Asian security situation with India, appreciated the Pakistani security forces' offensives against Islamist militants in recent months.
"Pakistan is a sovereign country and it is up to Pakistan when and where to launch an operation," the US defence secretary told reporters here.
The remarks came hours after Pakistan's chief military spokesman ruled out any new offensive in the next six to 12 months, saying the military needed the time to consolidate its gains.
"We (Washington and Islamabad) are in the same car on the issue but Pakistan is on a driving seat, having its foot on the accelerator," Gates said.
There has been growing pressure on Pakistan to expand an ongoing offensive in the South Waziristan tribal district to adjacent North Waziristan, a stronghold of militants associated with the insurgent group known as the Haqqani network.
The tribal belt is described as the hub of global terrorism from where the Al Qaeda and Taliban militants mount deadly assaults on the Western forces operating in Afghanistan.
"This area has a myth for Al Qaeda people because they used this area to defeat a superpower, therefore the Al Qaeda core will remain in these areas," Gates said.
The US has stepped up missile strikes on militant hideouts in the rugged territory in recent months, particularly after a suicide attack on a US intelligence centre in eastern Afghanistan killed seven CIA agents Dec 30.
A video of the Jordanian bomber's farewell message appeared within days. In the video, he was shown sitting next to Pakistani Taliban chief Hakimullah Mehsud, giving credence to the strengthening links between Al Qaeda and Pakistani militants.
Pakistan publicly opposes the drone attacks, complaining that they violate its territorial sovereignty and fuel support for the militants.
Islamabad has been asking Washington to provide it with drones so that its forces could take out the hostile targets themselves, removing the US involvement in the fight inside the tribal region.
Gates confirmed that the US was considering providing unarmed pilotless aircraft to Pakistan for reconnaissance missions.
He said earlier that the US would not abandon the lone nuclear-armed Islamic nation in the fight against terrorism, stressing that it was now in the relationship for the long haul.
Analysts say Pakistan is vital for the success of the new US strategy to win the fight against Taliban insurgency in Afghanistan.