Malik Ishaq was taken into "protective custody" for a month under the Maintenance of Public Order law from his residence in Rahim Yar Khan district, 400 km from Lahore.
Before the arrest, Ishaq held an hour-long meeting with district police chief Sufail Zafar and agreed to "surrender", sources said.
Ishaq also invited reporters to his residence before his arrest and told them that he would continue his "mission".
He claimed: "I have no link with the carnage in Quetta. We want peace in the country."
A majority of the victims were members of the minority Shia Hazara community. On January 10, twin suicide bombings by the LeJ killed 92 Shia Hazaras in Quetta.
However, Ishaq claimed authorities were cracking down on groups like the Ahl-e-Sunnat Wal Jamaat for the incidents in Quetta.
The ASWJ is considered a front for the banned Sipah-e-Sahaba, a sister organisation of the LeJ.
Ishaq claimed dozens of "innocent" ASWJ clerics had been arrested and this was being done at the behest of Interior Minister Rehman Malik.
He further claimed some 600 clerics and workers of the ASWJ had been killed in Karachi during the past three months.
He asked Supreme court Chief Justice Iftikhar Chaudhry to take suo motu notice of these killings.
"The judiciary should listen to both sects (Sunnis and Shias) and we will accept its decision," he said.
Officials said Ishaq is likely to be shifted from Rahim Yar Khan to Lahore.
Ishaq was linked to the murder of 70 Shias but was acquitted in a majority of cases registered against him after witnesses were killed or refused to testify.
While still in prison, Ishaq was accused of masterminding the 2009 attack on the Sri Lankan cricket team in Lahore that killed eight persons.
Police have been accused of being soft on Ishaq as the ASWJ is considered a close ally of the PML-N that rules Punjab.
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