However, a ground offensive has yet to begin and may prove to be the army's toughest test since fighters turned on the state.
Nevertheless, Rehman Malik, the interior minister, in an interview in Singapore said a ground offensive was "imminent".
"There is no mercy for them because our determination and resolve is to flush them out," he said.
"They have no room in Pakistan, I promise you."
Malik said members of the Pakistani Taliban and al-Qaeda were suspected to have been behind Saturday's attack on army headquarters, which ended a week when suicide bombers struck in the capital Islamabad and Peshawar, killing more than 50 people.
He also said the offensive against the fighters in South Waziristan was no longer a matter of choice.
"It is not an issue of commitment, it is becoming a compulsion because there was an appeal from the local tribes that we should do the operation," Malik said.
In an interview with Al Jazeera, Imtiaz Gul, a political analyst, said he agreed that the government was correct to commence an offensive against South Waziristan.
"A lot of al-Qaeda and ideologically tainted people belonging to the Islamic movement of Uzbekistan under the patronage of the Taliban are sheltering there," he said.
But not everyone agrees. Zafar Jaspal, a Pakistani analyst, believes that Islamabad has concentrated too much on the Swat valley and South Waziristan.
"Till today, the government has no clear strategy on how to deal with the militants who are residing in southern Punjab," he told Al Jazeera.
"The person who was captured alive after [the GHQ attack] comes from Punjab, and other members of that group are also from Punjab ... certainly the government needs to have a parallel strategy - for Punjab as well as South Waziristan."