Al-Zawahiri told Pakistanis in a statement posted on the internet that there was "no salvation for you except through jihad" and called on them to rise up against the government.
"If you do not revolt, Musharraf will annihilate you. Musharraf will not stop until he uproots Islam from Pakistan," he said.
The mosque compound remains surrounded by troops behind barbed wire but journalists were allowed to see inside on Thursday.
"When we entered the mosque we were able to see on the outside all the glass was shattered," Kamal Hyder, Al Jazeera's correspondent in Islamabad, said.
"Inside the compound we saw walls peppered with gunfire ... you could smell the gunpowder inside and outside the compound."
The military showed journalists a massive arsenal of weapons including suicide vests, grenade launchers and mines.Remains found
Major General Waheed Arshad, military spokesman, said two suicide bombers had blown themselves up in the raid and two fully-primed suicide jackets packed with explosives that had not been detonated were found.
|The walls of the Red Mosque were |
riddled with bullet holes [AFP]
He showed journalists a burned-out room in the school where he said a suicide attacker had blown himself up as troops tried to get in.
The army found the bomber's head and five of the charred bodies inside the room, he said.
Arshad said that the badly burnt remains of 19 people had been found and they could include women or children.
The government had previously said that no bodies of women and children had been found despite claims that hundreds of them had been held hostage inside.
Pakistani authorities also said they had not found any mass graves during their search of the site, despite Ghazi having said hundreds of people had been buried there.Suicide attacks
Meanwhile, two suspected suicide attacks in northwest Pakistan have killed at least seven people, including three police officers.
Almost 30 people have been killed in attacks on security forces and government targets in the northwest frontier region since the army laid siege to the Red Mosque, raising fears of a backlash.
A suicide bomb attack at the office of a senior government official in the North Waziristan tribal region killed two people, a witness wounded in the blast said.
"A man dressed in black blew himself up when he was stopped by an office worker in Khan's office," Sher Zaman told Reuters news agency from his hospital bed in Miranshah.
Another suicide attack targeted a police vehicle in the town of Swat town killing five, including three policemen, Shamsul Qamar, an official at the police control room in Swat, said.