About 1,300 suspected militants were arrested in a sweep of hideouts in Punjab, police said Friday.
The roughly two-week operation comes despite the provincial law minister's defence of some groups designated as terrorist organisations and banned by Pakistan but resurrected under new names.
Rana Sanaullah also embraced some sectarian leaders whose groups have been accused of fomenting violence against minority Islamic sects, raising questions about his commitment to ridding Punjab of militants.
Two police officials, speaking on condition of anonymity because of the sensitivity of the operations, said another 36 'militants' died in shootouts with police and in paramilitary operations since the sweep began last month.
In an interview with The Associated Press, however, Sanaullah questioned the label of terrorist for anti-Indian militant groups like Lashkar-e-Taiba, which has resurfaced as Jamaat-ud-Daawa.
Last month, Pakistan placed Hafiz Saeed, a declared terrorist with a US-imposed $10 million bounty on his head, under house arrest, yet Sanaullah questioned allegations against Saeed.
"They are related to Kashmir. They feel Indian brutality in Kashmir is unacceptable," he said of Saeed and his followers, adding that Pakistan's courts have twice freed Saeed saying there was no evidence of his involvement in terrorism activities.
Saeed is among India's most wanted and is accused of masterminding attacks inside India and Indian-held Kashmir.
"Why is the world not concerned about India's violence in Kashmir?" Sanaullah asked. "There is no evidence of Saeed's involved in state terrorism."
In an interview, Saeed's spokesman Yahya Mujahed denied Saeed's affiliation with the outlawed Lashkar-e-Taiba.
Analysts and critics say the Punjab government is sheltering sectarian and jihadi groups headquartered in its most populous province, while using the crackdown to target ethnic Pashtuns from tribal regions that border Afghanistan.
Sanaullah said police were searching out areas in Punjab dominated by ethnic Pashtuns and unregistered Afghan refugees because some of the worst attacks carried out in the provincial capital of Lahore involved residents of the tribal areas. He cited last year's Easter attack in Lahore that killed more than 75 people, including Christians, saying 11 men arrested in connection with the suicide attack were from Mohmand and Bajour tribal regions.
"They are from FATA (tribal areas) so we (have decided that we should) do action against those areas where people from Bajour and Mohmand are and where Afghan refugees who are not registered are residing," Sanaullah said denying his government is employing profiling in its crackdown that targets ethnic Pashtuns.
"Ironically, Punjab tops all other Pakistani territories in terms of religious/extremist/outlawed groups density; as many as 107 of the 240 or so socio-politically lethal groups are headquartered in the province, with 71 in Lahore and around alone, including the one that is an eye-sore for Indians," said Imtiaz Gul, executive director of the Islamabad-based Centre for Research and Security Studies (CRSS). He was referring to Hafiz Saeed's Lashkar-e-Taiba, which has been resurrected as Jamaat-ud-Daawa,.
"Out of this, 148 are sectarian outfits while 24 are jihadi organisations, while 12 outfits claim to work for the revival of an Islamic (caliphate) as their objective," which is the aim of the Islamic State group, Gul said in a blog published this week on the CRSS site.
