The detainees include foreigners and the local Pashtun tribesmen who have been sheltering them, said Lt. Gen. Safdar Hussain, who is in charge of the sweep.
Hussain said an estimated 400 to 500 militants were still fighting from heavily fortified compounds in the tribal South Waziristan region, using mortars, AK-47s, rockets and hand-grenades in a face-off with troops.
"These people have been here for a long, long time. They are extremely professional fighters," he said. "They have tremendous patience before they open fire."
Meanwhile, a senior Pakistani army officer told The Associated Press that an American helicopter fired rockets at a car in the Alawarai Mandi district of North Waziristan, just one mile from the Afghan border. Three people inside were injured, the officer said, speaking on condition of anonymity.
He said it was not clear if the Americans were after a specific target or knew they had crossed into Pakistani territory.
Lt. Col. Bryan Hilferty, the main spokesman for U.S. forces in Afghanistan, disputed the claim.
"There are no American or combined forces over there," he said.
The issue is a sensitive one. Pakistani President Gen. Pervez Musharraf is a staunch U.S. ally, but he has steadfastly insisted that no American troops be allowed on Pakistani soil. If confirmed, an attack by the Americans would be likely to enflame deep hostility.
An Afghan security official gave a different version Saturday. He said American helicopter gunships and Afghan troops repelled a Taliban attack near the eastern border with Pakistan, killing three suspected Taliban fighters.
The attack occurred in the Bermal district of Paktika province, across the border from a massive ongoing Pakistani offensive against al Qaeda in that country's South Wazirstan tribal area.
Zakim Khan, Paktika province intelligence chief and an Afghan militia commander, said suspected Taliban attacked Afghan checkpoints with rockets Friday night.
Afghan troops responded with AK-47 fire, Khan said. American forces with Afghans brought in helicopter gunships, firing upon the attacker position, he said.
Four hours of fighting left three Taliban dead and eight injured, with no casualties among the Afghan soldiers or Americans, Khan said.
Khan said he believed the attack came from Pakistan, but gave no details.
U.S. special operations forces and others are in the Afghan-Pakistani border region in a stepped-up campaign to capture Taliban and al Qaeda fugitives hiding in the mountains there, and to close escape routes from hide-outs in Pakistan.
On March 5, U.S. special operations snipers killed nine alleged Taliban in the area after 30 to 40 of the fighters allegedly tried to flank an American-Afghan position, the U.S. military said.
The Pakistani military showed journalists 40 prisoners, all blindfolded and with their hands tied, sitting under heavy guard in the back of a military truck in Wana, the main town in South Waziristan.
The army also displayed the body of one suspected militant wrapped in a white blanket, and said it had intercepted phone conversations from within the compounds in Chechen, Uzbek and Arabic.
Hussain said troops were convinced the compounds held a "high-value" target, given the level of resistance, but could not confirm it was al-Zawahri, although he didn't rule out that someone might have escaped.
"With this level of resistance, even after 48 hours (of the latest bombardment), I believe the high-value target is still there," he said.
Hussain said a Chechen fighter had been arrested with a book on chemistry and explosives. He said he suspected many of the militants were foreigners, but that others were from Pakistan's Yargul Khel tribe.
"I'm determined to punish this tribe and make them an example for the entire South Waziristan agency," Hussain said.
As he spoke, Cobra attack helicopters hovered overhead, some swooping toward the battle zone.
The fighting has forced an exodus of thousands of terrified civilians. Many have taken refuge in Wana, but there were indications Saturday the battle was following close on their heels.
Loud explosions and gunfire could be heard early Saturday in Gangikhel village, a hamlet of simple mud dwellings just three miles west of Wana. Previous fighting in Kaloosha, Azam Warsak and Shin Warsak was about twice that distance from Wana, close to the border with Afghanistan.
Brig. Mahmood Shah, chief of security for tribal areas in northwestern Pakistan, told AP that some of the prisoners had been taken for interrogation to the provincial capital, Peshawar.
Security officials said the men included Pakistanis, Arabs, Chechens, Uzbeks and ethnic Uighurs from China's predominantly Muslim Xinjiang province, where a separatist movement is simmering. No senior al Qaeda leaders were believed to be among them, but authorities hoped they would provide a better picture of the terrorists' heavily fortified lair.
"Our people are interrogating them to determine who these terrorists are," Shah said. "Some of them are foreigners."
Sultan said the Pakistani forces were joined by "a dozen or so" American intelligence agents in the operation. U.S. satellites, Predator drones and other surveillance equipment hovered overhead.
Sultan put the number of troops killed at 17, most in the disastrous initial assault on Tuesday. But other military and intelligence officials said many more had died in the heaviest fighting on Thursday and Friday, and that about a dozen soldiers were missing and feared taken hostage.
An Afghan intelligence official with connections in Pakistan's tribal region also told AP that al-Zawarhi was believed in the area of the Pakistan operation, in South Waziristan.
Osama bin Laden is believed farther north, in North Waziristan, closer to the Afghan border city of Khost, he said. There was no firm intelligence on the terror chief's exact location, however.
Jawed Ludin, a spokesman for Afghan President Hamid Karzai said U.S. and Afghan troops captured "semi-senior" terrorist leaders on their side of the border in recent days, though there was no confirmation of that from the Americans. Ludin declined to give details of who might be in custody.
Defense Secretary Donald Rumsfeld praised Pakistani forces for their work, but said in an interview Friday on CNN's "Larry King Live," that it was not clear whether al-Zawahri was there.
"It's not clear to me who's there, if anybody, but certainly there are an awful lot of fine Pakistani forces working hard," he said.
Interior Minister Faisal Saleh Hayyat told AP that authorities hoped to wrap up the operation by Sunday afternoon. But Shah said the going was slow, with soldiers proceeding cautiously from house to house.
"We are trying to avoid collateral damage to the civilian population. It might take some time," he said.
Residents have denounced the army operation as heavy-handed and against the centuries-old traditions in the semiautonomous tribal region, which has fiercely resisted occupation by Afghan rulers, British colonialists or Pakistani army troops.
Under pressure from Washington, Pakistan has sent 70,000 troops into the tribal zone and conducted several raids, though nothing on the scale of this week's operation.