Information Minister Shaikh Rashid Ahmad said on Tuesday the latest operation was launched near Wana, nearly 300km north-east of where al-Qaida chief Usama bin Ladin was reported to be hiding.
Troops destroyed two houses with cannon fire in the village of Zarai Letta, about 15km west of the town of Wana, while 14 military helicopters flew overhead. Wana is 360km south-west of Islamabad.
Seven suspects were seen being driven away in military vehicles, but it was unclear if they were foreigners or local tribesmen. Intelligence officials said 25 people, including women, had been detained.
"We are trying to establish their identity but initial investigations suggest there could be some Uzbeks, Chechens and Arabs among them," one said.
Military spokesman Major-General Shaukat Sultan said the operation followed a tip-off about the presence of "foreign terrorists" who failed to surrender by a 20 February deadline.
"We have launched an operation against foreign terrorists," Ahmad said on Tuesday.
"... initial investigations suggest there could be some Uzbeks, Chechens and Arabs among them"
Unnamed intelligence official,
Asked whether the operation was intended to hunt bin Ladin, he said: "It is against foreign terrorists."
Pakistan, a key US ally, has arrested more than 500 al-Qaida suspects and handed them over to the US over the past two years.
Authorities in South Waziristan have been pressuring tribesmen in recent months to hand over al-Qaida suspects and Taliban fighters hiding in the region. In October, eight al-Qaida or Taliban suspects were killed there.
Those killed in that operation included Ahmad Saeed Khadr, an Egyptian-born Canadian thought to be an al-Qaida financier, and a top Chinese Islamist Hasan Mahsum.
Tuesday's operation came hours after US President George Bush vowed to track down members of al-Qaida.
A day earlier, US military officials said the whereabouts of al-Qaida leader Usama bin Ladin remained a mystery and the focus of hunts is in border regions where many Islamic and Taliban fighters are believed to be hiding.
"We are on the hunt for al-Qaida," Bush told a meeting of US governors at the White House.
"It requires all assets, intelligence assets and military assets, to chase them down and bring them to justice, and we're going pretty good - better than pretty good," he said.