The attack on the base on Friday was the deadliest ever militant attack on a Pakistani military installation and is likely to undermine already rocky ties with Afghanistan.
Hours after the attack, military spokesperson Asim Bajwa pointedly noted that communications intercepts showed the Taliban gunmen were being directed by handlers in Afghanistan.
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Saturday's air force raids targeted militant bases in the Tirah Valley, which straddles the Afghan border and is a main smuggling route between the two countries, two security officials said.
"All those killed in the bombing were Pakistani militants," said one security official in Peshawar.
On Friday, 13 gunmen stormed the Badaber air base, about 10 kilometres south of Peshawar in an attack a Tehreek-e-Taliban (TTP) spokesperson said was retaliation for bombing raids on their bases along the Afghan border.
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Police said they picked up around 50 residents living near the base on suspicion of helping the militants organise the attack.
Shafqat Malik, head of the Peshawar bomb squad, said the attackers carried enough firepower to occupy the base, but that some of their weapons had malfunctioned. Each man had an assault rifle, two improvised explosive devices, and several rocket propelled grenades, but some of the grenades misfired, he said.
"Their mission was occupation of the air base," he said.
Pakistan launched an offensive to dislodge TTP from North Waziristan in 2014 and there has been fighting in various places, including the Tirah Valley, since then.
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For years Pakistan and Afghanistan have traded accusations of not doing enough to stamp out insurgents on either side of their long, porous border.
Last month, Afghanistan blamed Pakistan for not doing enough to counter militants who carried out a series of attacks in the Afghan capital, Kabul.
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