"The government is targeting jihadi (holy warrior) groups at the behest of America and India. We condemn the move," said spokesman Mushtaq Askari of the Al-Badr Mujahedeen, which is fighting to end Indian rule in the disputed region of Kashmir.
"Any crackdown or restrictions won't hurt our struggle. Our Kashmir jihad will continue," Askari said.
The arrests came amid tensions between Pakistan and India, which accuses Pakistani intelligence and two Islamic groups -- Lashkar-e-Tayyaba and Jaish-e-Mohammed -- of being behind a Dec. 13 attack on its Parliament. Pakistan denies involvement.
Fourteen people, including the five attackers, were killed in the parliament attack. The incident prompted the two South Asian nuclear rivals to send troops to their border in the largest military buildup since their 1971 war.
In an address to the nation on Saturday, Pakistani President Pervez Musharraf banned five Islamic groups, including the Lashkar-e-Tayyaba and Jaish-e-Mohammed. Although he said the crackdown on extremism was due to internal security concerns, the move was likely to ease tensions with India.
Most of those arrested belonged to the most violent Sunni Muslim group, Sipah-e-Sahaba, or Guardians of the Friends of the Prophet.
The other two banned groups are Tehrik-e-Fiqah Jafria, or the Movement for the Imposition of Shiite Law, and Tehrik Nifaz Shariat-e-Mohammedi, the Movement for the Enforcement of the Law of the Prophet Mohammed. Both are Shiite Muslim groups.
Some of the outlawed groups are active in the Indian part of Kashmir. Musharraf, in his hourlong address to the nation, vowed that "no organization will be allowed to indulge in terrorism behind the garb of the Kashmiri cause."
Overnight, police raided the Al-Badr Mujahedeen office in Rawalpindi, 12 miles from Islamabad, and arrested its secretary general, Qari Ejaz Ali, Askari said by telephone. He said about 70 members had been arrested nationwide.
