Information Minister Sheikh Rashid Ahmed said authorities are still trying to determine the authenticity of the tape, which was released on the Arabic satellite channel Al-Jazeera on Thursday.
On Friday, a CIA official, who spoke on the condition of anonymity, said "after conducting a technical analysis, the CIA has assessed that the voice on the tape … is likely that of Ayman al-Zawahri."
Ahmed said the tape's call for the overthrow of President Gen. Pervez Musharraf was ludicrous.
"Pakistan does not take orders from anybody," Ahmed said at a news conference in the capital. "We condemn and reject the statement made by Ayman al-Zawahri. The entire nation is fully behind the policies of President Pervez Musharraf."
In the audio tape, the speaker called Musharraf a "traitor" and said Pakistani soldiers should disobey him.
"Every Muslim in Pakistan should work hard to get rid of this client government, which will continue to submit to America until it destroys Pakistan," the speaker said.
The speaker on the tape sounded like al-Zawahri and made references to the Islamic holy book, the Quran, which is known to be al-Zawahri's style.
The tape was released as Pakistan pressed on with a terror sweep in South Waziristan, near the Afghan border, that is the nation's biggest counterterrorism operation since Musharraf threw his support behind the U.S.-led war on terrorism in late 2001.
Last week, Musharraf said a "high-value" terrorist suspect could be hiding in tribal South Waziristan, where hundreds of militants have battled thousands of Pakistani forces. The government did not identify the suspect, but a number of senior officials privately said they believed it could be al-Zawahri.
The discovery of a mile-long tunnel leading out of the battle area has led to speculation that any important terror fugitives may have escaped.
Ahmed vowed that the campaign would continue.
"Dozens of Pakistani soldiers were killed during the military operation," he said. "So it will continue until the terrorists who have scattered in our tribal areas are either apprehended or eliminated."
Musharraf is facing rising political opposition to the Wana operation, which reflects widespread anger in this conservative region about the military deployment and growing unease across Pakistan about his support for Washington.
Supporters of the hardline coalition Mutahida Majlis-e-Amal gathered peacefully in Peshawar, Karachi, Lahore, Multan and Quetta to protest the operation. The largest rally in Rawalpindi, near the national capital Islamabad, drew about 1,500 people.
"We condemn this operation because it is aimed at appeasing the Americans," said Sirajul Haq, a senior minister in North West Frontier Province where the tribal areas are located. He was speaking at the Peshawar rally.
On Friday, troops demolished 40 to 50 of the mud-brick, fortress-like homes of tribesmen accused of providing protection to al Qaeda fighters, officials said on condition of anonymity. The homes were destroyed in several villages near Wana, the main town in South Waziristan.
Interior Minister Faisal Saleh Hayyat told lawmakers on Thursday that more than 20 terrorists were confirmed killed and that he expected 30 to 35 more bodies of terrorists would be recovered as the operation concludes.
Officials have reported at least 30 Pakistani army and paramilitary troops have been killed, and a dozen more held captive.
At least 163 people have been arrested, many of them tribesmen. But Ahmed insisted the sweep was aimed at foreigners, not Pakistanis.
"This operation is not against the tribesmen. This is only directed at the terrorists," he said.
The crackdown in Wana has provoked several attacks against the army outside the battle zone.
Tribesmen on Friday turned over the bodies of eight soldiers missing since a March 22 rocket attack on their convoy in Jandola, 30 miles east of Wana. On Wednesday, three rockets were fired at the provincial capital, Peshawar, slightly injuring two people.
Ahmed acknowledged mistakes were made in the lead-up to the operation, which began with a disastrous March 16 assault in which 15 paramilitary troops died. He said the government had been too soft on the terrorists, offering them an amnesty and several months to surrender.
"We admit that we started this operation late," he said. "We kept showing hospitality and offering them amnesty, and they continued strengthening their positions."
Elsewhere, two small bombs exploded Friday in a southern Pakistani city, but no damage or casualties were reported, police said.
No one claimed responsibility for the blasts in Jacobabad, about 250 miles northeast of the port city of Karachi, said Deen Mohammed Baluch, a senior police official.
He said the explosions occurred in a commercial area of the small city, several miles from Jacobabad air base, one of Pakistan's main military facilities.
The base is being used by U.S. troops to back anti-terrorism operations in neighboring Afghanistan.
In Kashmir, five people were killed in an overnight gunbattle as government forces laid siege to a village used by Islamic guerrillas as a hideout in Indian-controlled Kashmir, police said Friday. India has accused Pakistan of backing those guerrillas, but Pakistan contends it only provides moral support.
Al-Zawahri is a physician widely consider a mentor to Osama bin Laden. he has frequently been seen on videotapes with the al Qaeda leader. The founder of Egyptian Islamic Jihad, he is high on the U.S. list of most wanted terrorists, with a $25 million price on his head.