Shafi, in his 80s, is a former student of India's Darul Uloom Deoband.
He is the chief of the newly-floated Hefazat-e-Islam or 'Protectorate of Islam' which enforced a "Dhaka siege" programme to mount pressure on the secular Awami League-led government to implement their 13-point demand, including the enactment of a blasphemy law to punish those who insult Islam and its Prophet.
"He (Shafi) was picked up from Jamiatul Arabia Madrasah at Lalbagh along with four others and to be sent back to Chittagong," a senior police official told PTI.
They said Shafi was escorted to a police car which apparently headed towards the Hazrat Shahjalal International Airport to be flown to the southeastern port city Chittagong.
The development came as riot police and paramilitary troops overnight chased thousands of Hefazat-e-Islami members off the capital. At least 14 people were killed in clashes in the past 48 hours.