The ferry was only licensed to carry 85 passengers, but was packed with more than 200 people returning from their villages following the Muslim Eid holiday.
Rescuers have so far recovered 48 bodies from the water, but have not been able to locate the wreckage in the fast-flowing river. Around 60 are still missing.
The government has charged A. B. Siddique Kalu and five others, including the ferry captain, with culpable homicide not amounting to murder over the disaster. If found guilty, they face up to ten years in jail.
"We have arrested him in (the port city of) Chittagong early today," Ziaul Ahsan of the Rapid Action Battalion, Bangladesh's elite security force, said.
Bangladeshi rescuers abandoned their search for the ferry on Monday (August 11) after a week of fruitless efforts amid ongoing bad weather.
Ferry accidents are common in Bangladesh, with overcrowding and poor ship design and maintenance often to blame.