In a continuing operation that began early on Thursday in South Waziristan district, at least 10 suspected Afghan fighters were also nabbed.
"The fighting is still going on," Pakistani Major General Faisal Alavi said.
The operation under way in South Waziristan district was primarily aimed against foreign elements involved in attacks against coalition forces in neighbouring Afghanistan.
"These foreign elements were causing nuisance to the local inhabitants," military spokesman Major General Shaukat Sultan said.
"Last night we received credible information of al-Qaeda hideouts. The Pakistani army acted swiftly and launched an operation," he said.
The spokesman said the operation commenced early on Thursday morning and was progressing well.
Afghan officials have repeatedly pointed to South Waziristan as a troubled spot, from where al-Qaida and Taliban fighters launched attacks deep inside Afghanistan.
Pakistani officials, however, did not give details of how many troops were deployed in the operation or how many al-Qaida suspects they were moving against.
Local residents in the town of Wana, the biggest town in the region, said helicopters were taking part in the operation.
"We have seen some 20 helicopters operating in the area," a resident said.
State-run Pakistani television said the operation was being manned exclusively by Pakistani troops. No foreign agency or foreign troops were involved, it said.