A court in Dhaka formally accepted charges against Sohel Rana, 35, and the others in connection with the country's worst ever industrial disaster.
"We've charged 41 people including the owner of the building, Sohel Rana, with murder over the collapse of Rana Plaza in April 2013," lead investigator Bijoy Krishna Kar told AFP, adding that all face the death penalty if convicted.
Among those charged are seven owners of factories housed in the complex and 12 government officials responsible for safety and inspections.
Police asked the court to issue arrest warrants for 25 people including six government officials after they absconded.
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"It is the biggest industrial disaster in Bangladesh's history. And all 41 of them have collective responsibility for this mass killing of more than 1,100 innocent people," Kar said.
Rana became Bangladesh's public enemy number one after survivors recounted how thousands of them were forced to enter the compound at the start of the working day despite complaints about cracks appearing in the walls.
Rana and 17 others were also charged with violating the building code, for extending the six-storey structure - which was initially approved as a shopping centre - into a nine-storey factory complex.
"Rana Plaza was built flouting construction rules and it was extended without proper structural changes. And when it was turned into a factory complex, it was loaded with heavy machinery such as a generator. No wonder the building collapsed," Kar said.
"That illegal extension violating all construction (regulations) was the seed of this massive disaster," Kar said yesterday.