The court in Dhaka issued the warrants for Delwar Hossain and his wife Mahmuda Akter over the blaze in 2012 at the Tazreen factory, where workers stitched clothes for Western retailers.
"Dhaka's senior judicial magistrate Wasim Sheikh issued the warrants of arrest against the two fugitive owners, Delwar Hossain and his wife Mahmuda Akter, and four other company officials for the Tazreen factory fire," prosecutor Anwarul Kabir told AFP.
The fire on November 24, 2012, shone an international spotlight on appalling safety conditions in an industry worth more than $20 billion a year.
The factory, in the Ashulia industrial district, supplied clothes to a variety of international brands including US giant Walmart, Dutch retailer C&A and ENYCE, a label owned by US rapper Sean "Diddy" Combs.
Kabir said the court accepted charges by police against all 13 implicated in the fire after officers earlier this month completed a 13-month investigation into the tragedy.
"The owners and 11 others have been charged with arson, culpable homicide not amounting to murder and death by negligence," Kabir said, adding that all the accused face a maximum life term in prison.
The six whose arrest was ordered were not in court or in custody.
Police last week said it was possibly the first time a garment plant owner has been charged over a fire at one of the nation's 4,500 factories, where deadly accidents are common.
Factory owners are rarely charged over such tragedies in the sector, which is a mainstay of the impoverished country's economy, accounting to up to 80 percent of Bangladesh's exports.
The country suffered an even greater tragedy just months later in April when the Rana Plaza garment factory complex collapsed in Dhaka's outskirts, killing 1,135 people in the world's worst industrial disaster.