Qari Muhammad Nur was arrested with three associates last week in a raid on an Islamic school in the central city of Faisalabad.
Faisalabad police said he was brought to a hospital on Wednesday where he died of "heart failure". But intelligence officials and Islamic groups said Nur died after he was tortured and that television pictures showed bruises on his body.
"The death of Qari Nur Muhammad and reports that there were marks of torture on his body are a cause for grave concern," the Human Rights Commission of Pakistan said in a statement on Friday. "It is not the first incident of torture in custody."
The rights group said the failure of authorities to abide by the law when dealing with armed fighters suspects was "uncivilised" and could "only produce negative results".
Pakistani intelligence officials said Nur was suspected of helping al-Qaida members find accommodation in Faisalabad.
The army has launched another
push against suspected fighters
He was arrested in a crackdown launched since the arrest in Pakistan last month of an al-Qaida computer expert, Muhammad Naim Nur Khan, who has proved a key source of information on the identity of operatives from Usama bin Ladin's organisation.
Khan's arrest is said to have led to the detention of more than 60 suspected fighters in Pakistan and revealed plans for attacks on British and US targets.
In another development, Aljazeera's correspondent in Islamabad, quoting tribal sources, reports that Pakistani government forces backed by helicopters are pressing on with their offensive against suspected al-Qaida fighters in a number of areas in South Waziristan.
Witnesses talked of clouds of smoke rising from several mountain sites that were subjected to heavy bombing on Saturday morning.
On Friday, fierce fighting had erupted in the province's Shakai region, between Pakistani Army soldiers on the one hand and suspected al-Qaida fighters and tribesmen sympathetic to their cause on the other hand.