Saeed was arrested on Wednesday by a group of counterterrorism department police at the Kamoke toll plaza, about 50km north of Pakistan's second city Lahore, JuD spokesman Nadeem Awan told Al Jazeera.
Both designations blamed him for the November 2008 Mumbai attack in which 166 people, including six American citizens, were killed.
LeT members were involved in 26/11 terrorist attacks in Mumbai in 2008 that killed 166 people, including six U.S. citizens.
Only a handful of peripheral planners - and one gunman captured after the attack - have been convicted.
Many see Saeed's arrest as Pakistan as acting under Financial Action Task Force or FATF's pressure who chose to keep Islamabad on greylist after missing two deadlines to meet its anti-terror financing commitments.
Saeed, who has several cases pending against him, was travelling to Gujranwala from Lahore to appear before an anti-terrorism court when the arrest took place, officials said, adding that he had been moved to an unknown location.
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Mr Saeed's spokesperson, Nadim Awan, denounced the arrest and said the cleric had dissociated himself from LeT in 2001 and has had no links with the organisation since then. Saeed later said he left the group and founded the Jammat-ud-Dawa charity, which has been described as a front for militant activities.
Mr Awan said they would challenge Mr Saeed's arrest before a higher court. "Great pressure has been exerted over the last two years to find him!"
His arrest came just days ahead of Prime Minister Imran Khan's first official visit to Washington to meet President Trump.
"We want real action, not these kinds of steps that are reversible".
India sees Pakistan government's action with suspicion and the so-called crackdown against terrorists is seen as diversionary tactics.
Saeed has been repeatedly detained but always freed and, in general, courts seem reluctant to prosecute members of these militant groups, often releasing them on technicalities or for lack of evidence.