The military declared the operation over on Sunday, and claimed it was a success. Some 167 suspects were arrested, but hundreds of other militants are still at large, including Uzbek terrorist leader Tahir Yuldash, who was reportedly injured in the assault.
Army spokesman Maj. Gen. Shaukat Sultan said that 63 militants had been killed in the operation, and 167 arrested: 73 foreigners and 94 locals. He did not identify the foreigners' nationalities, but earlier security officials have said Uzbeks, Chechens and Arabs were among them.
He described the Uzbek leader Yuldash as No. 10 in the al Qaeda hierarchy.
The spokesman said that 46 troops were killed and 26 injured.
Villagers have begun filing back into their homes after seeking shelter in Wana and other villages during the operation, when thousands of Pakistani forces battled hundreds of foreign and local militants.
"I do not know whose rocket hit my house. I do not know who looted my home during the military operation, but I think the government is responsible for it," said Mohammed Alam, 43, a resident in the Azam Warsak area, which was a focus of the military operation.
He returned Monday and found parts of the roof and walls had caved in. He said his house had been stripped of belongings.
"Why did the army and the government ask us to leave if they could not protect our houses?" Alam said.
Sultan said troops had only demolished the homes of tribesmen who were sheltering terrorists, but conceded that some other houses could have come under attack and said the provincial authorities would look into it. He denied the claims of Alam and other tribesmen of looting.
"Such things did not happen when army was there," Sultan said Monday.
Another returning resident, Malik Sabir Khan, 54, claimed his house was damaged by rockets fired by the army. "There was no al Qaeda man at our house. Why did the army hit our house?" he said.
While Pakistani troops have withdrawn from the target area of the operation, they have not pulled out of South Waziristan.
Sultan said some of the militants had "dispersed into smaller groups" and they would not be allowed to regroup. He said Pakistani paramilitary and army forces in the region remained "combat ready."
"We are keeping an eye on them. When our intelligence picture is complete, we may go and nab them," he said.
Brig. Mahmood Shah, security chief for Pakistan's tribal areas, said Sunday that 500-600 suspected militants still might be hiding along the border with Afghanistan.
President Gen. Pervez Musharraf, a key ally of the United States, has sent 70,000 troops to the border with Afghanistan since the Sept. 11 attacks to prevent cross-border attacks — the first such deployment since independence from Britain in 1947. Prior to Sept. 11, Pakistan had long been a key backer of the Taliban.
U.S. and Afghan forces have been deployed on the other side of the border as part of a new offensive against al Qaeda and Taliban forces there.
When the clash between soldiers and militants first erupted, there were reports that al Qaeda No. 2 Ayman al-Zawahri may have been among them. The reports were never confirmed.
Pakistan's government last week angrily denounced an audiotape, which the CIA suspects contained the voice of al-Zawahri, that called for Musharraf's ouster. He has survived at least three recent assassination attempts.