Two women were killed and several others were injured in the June 2012 cave-in at the Algo Centre Mall in Elliot Lake.
Ontario Provincial Police said 64-year-old Robert Wood was charged with two counts of criminal negligence causing death and one count of criminal negligence causing bodily harm.
Wood's family said he had no comment on the charges.
"This was a unique, complex and challenging investigation which took considerable time to process evidence and being precise in the application of criminal law," said Det.-Supt. Dave Truax.
Adding to the intricacy of the case was the "multitude of various specialists" brought in to help police in the case.
"This was very unique where it involved Ontario Provincial Police retaining independent third-party engineers and contractors in order to assist us in our criminal investigation," said Truax, adding that a company which analysed concrete and another that created a 3-D diagram of the mall were also used.
Truax wouldn't say if charges against others were pending but emphasized that the criminal investigation was ongoing.
"We recognize that there are many questions still unanswered about the events of that day," he said. "I would like to thank the people of Elliot Lake for their patience, their resiliency during this very difficult time."
Doloris Perizzolo, 74, and Lucie Aylwin, 37 were killed in the collapse which triggered an intensive rescue operation involving heavy-duty machinery and a specialized rescue team.
A lawyer representing the families of the victims welcomed Friday's charges.
"Any degree of resolution that they experience from any legal proceedings against the parties who are responsible will be very much appreciated by the families," said Roger Oatley, adding that the families remained eager to know if others would be charged.
A judicial inquiry into the collapse concluded last October after hearing from 125 witnesses over 117 days. A report from those proceedings is due before Oct. 31 this year.
The inquiry heard the roof-top garage of the poorly designed structure leaked from the beginning, and decades of water and salt penetration caused severe rusting of its steel support structure.
Ultimately, a weld which was subject to years of corrosion snapped, sending one vehicle and concrete crashing into the mall below.
Yet, the inquiry heard, Wood declared the centre structurally sound just weeks before it collapsed.
In a 2011 conversation relayed to the inquest, Wood was cited telling a prospective buyer it would cost $1.5 million to fix the mall's roof and reportedly warned the structure had to be fixed or the roof would cave in.
However, Wood told the inquiry he could barely recall any such conversation.
Subsequently, in May 2012, Wood told the mall's owner that steel supports at the shopping centre showed surface rusting, but were otherwise "structurally sound," the inquiry heard.
That assessment followed an inspection of the property in which Wood noted "no visual distress.''
Wood later admitted changing his final May 3, 2012, inspection report after he and his partner signed off on it.
The changes included removing photographs he had taken in a mall store showing yellow tarps strung up to collect water leaking from the roof and a corroded steel beam. He also removed a reference to "ongoing'' leakage.
The changes were made at the request of the mall owner, Wood told the inquiry, as the man was apparently unhappy the mall would look bad when he was trying to get refinancing for it.
The inquiry also heard Woods testify that the mall owner told him the mall's leaks were going to be fixed and the engineer said he "gullibly" believed the man.
Wood was stripped of his professional engineering licence in November 2011 after admitting to misconduct unrelated to the mall.
He continued to practise as a "graduate'' engineer and owner of M.R. Wright based out of Sault Ste, Marie, Ont. with restrictions on what he could do. His 40-year career ended shortly after the mall roof collapse.
Wood is expected to appear in court in Elliot Lake on March 25.
Follow @dianamehta on Twitter.