The Leicestershire Police named the men as 33-year-old Aram Kurd, the owner of the Polish mini-supermarket Zabka on the ground floor of the building, 32-year-old Hawker Hassan and 37-year-old Arkan Ali.
"All three have been charged with five counts of manslaughter and with arson with intent to endanger life," the police said in a statement.
They are being held in custody over the weekend and will appear before Leicester Magistrates tomorrow, it said.
"Throughout this complex investigation we have been urging journalists and members of the public not to speculate about the cause of the explosion. With three people now charged and due in court, it becomes even more important, for legal reasons, that this message is heeded," the statement said.
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The police have formally identified members of the Indian-origin family from Mauritius that were among the five people "missing", feared dead. Brothers Shane Ragoobeer, 18, and Sean Ragoobeer, 17, who lived in the flat above the Polish shop were identified following "detailed forensic enquiries conducted over several days".
The others killed in the explosion and ensuing fire on February 25 include 18-year-old Leah Beth Reek, Shane's girlfriend, and 22-year-old Viktorija Ijevleva, a shop-worker at the Polish mini-supermarket. An inquest into their deaths will be conducted at a later date.
Police have refused to comment on local media reports claiming the explosion at the two-storey building may have been caused by an illegal alcohol distillery.
Human remains were recovered from the ruins of the building after the blast, which was followed by a massive fire that injured several others on February 25.