Syed Munawwar Hasan, a religious leader, told the crowd: "Musharraf is going an extra mile to implement the agenda of America in this part of the world."
In the capital Islamabad, hundreds called for jihad and chanted "Musharraf is a killer" and "Glory be to the Red Mosque martyrs" at a rally organised by Pakistan's Mutahida Majlis-e-Amal, an alliance of religious political parties.
Maulana Abdul Ghafoor Hydri, the group's deputy leader, told the gathering: "This carnage will prove to be the last nail in the coffin of Musharraf's dictatorial rule in Pakistan.
"Now there will be Red Mosques everywhere in Pakistan."
Smaller rallies were held in Rawalpindi, Lahore, Peshawar, and elsewhere a day after Mutahida Majlis-e-Amal endorsed a call by 13,000 religious schools for a nationwide protest against the attack on the Red Mosque, or Lal Masjid, in Islamabad.
Ayman al-Zawahiri, deputy leader of al-Qaeda, and the Taliban in neighbouring Afghanistan have called for attacks, including suicide bombings, against government targets.
Abdul Aziz Ghazi, brother of Abdul Rashid Ghazi, the Red Mosque leader killed in the eight-day mosque siege, called for an "Islamic revolution".
Two suicide attacks were reported on Thursday, a day after the siege ended in a hail of bullets and explosions that wiped out armed students and possible Uzbek fighters inside the sprawling mosque compound.
Police on Friday raided a house in the northwestern town of Dera Ismail Khan and arrested three suicide bombers who were preparing for attacks, said Niaz Quereshi, a police spokesman.
Quereshi said five so-called suicide vests, 100 mortar shells, two rockets and one landmine were seized.
Violence across northwestern Pakistan has killed at least 35 people since the fighting at the mosque began last week, prompting the army to send troops to at least four parts of the region to contain the backlash.
Musharraf, speaking on television on Thursday night, said he was resolved to eradicate extremism across Pakistan.
"Extremism and terrorism will be defeated in every corner of the country," Musharraf said.
He said that madrassas will not be tolerated if they inculcate violence among students, like some under the Red Mosque's umbrella did.
|Musharraf on Thursday vowed 'war|
on extremists' in the country [AFP]
Tariq Azeem Khan, Pakistan's deputy information minister, said that the government has taken "appropriate steps to safeguard the lives and property of common people, and to ensure that no one damages public property."
On Friday, the Supreme Court ordered the government to release by Monday all persons arrested at the Red Mosque if they were not involved in major crimes.
Tariq Khokhar, deputy attorney-general, said that 632 people, including the wife of Red mosque leader Abdul Aziz and his two daughters, were arrested during the operation. Some 386 people have already been released.
Khokhar, quoting an official government report, said 102 people died in the Red Mosque violence, including 91 civilians and 11 military personnel. He said 248 were injured, including 204 civilians and 44 military.
Opposition figures claim the death toll is higher, but none has offered any evidence.
Qazi Hussain Ahmed, president of Mutahida Majlis-e-Amal, has claimed that between 400 and 1,000 civilians were killed.
Source: Al Jazeera and agencies