The engineer is alleged to have endangered a worker by providing "negligent advice," the ministry said.
The Ministry of Labour's Tom Zach told The Canadian Press the accused is Robert Wood, an engineer found guilty of professional misconduct in 2010.
Wood and colleague Gregory Saunders of M.R. Wright and Associates based in Sault Ste. Marie, Ont., inspected the mall in Elliot Lake, Ont., as recently as April, 2012.
A month later — just one month before the collapse — they wrote to say the mall was structurally sound despite finding rust on beams.
Wood could not be immediately reached for comment late Monday.
Last June, the roof-deck garage of the Algo Centre Mall caved in. Two women were killed and several others injured.
A judicial inquiry, at which Wood has standing, is currently probing the tragedy and provincial police are also investigating.
A second charge against the engineer relates to working in a manner "that may endanger a worker," according to the ministry.
Maximum penalties on conviction are a fine of up to $25,000 and/or up to 12 months imprisonment.
Wood is scheduled for a first appearance on May 15, at the Ontario Court of Justice in Elliot Lake.
Doug Elliott, who represents citizens of the town, said Monday he was not surprised at the charges.
"I know the Ministry of Labour was investigating everyone involved," Elliott said.
"Some of the engineers were concerned they could be charged."
Wood was an employee and shareholder with M.R. Wright, which is no longer in business.
The judicial inquiry under Commissioner Paul Belanger has heard evidence related to how the mall was poorly designed from the start, with its untried water-proofing system failing immediately on construction in 1980.
Residents and storekeepers in the mall spent years complaining about severe leaking that caused pieces of cement to crumble and beams to rust.
Nevertheless, several inspections — among them some done by professional engineers in the months before the collapse — failed to turn up any concerns about the impending disaster.
A forensic engineering report for the inquiry concluded that road salt and constant water penetration had created a "marine-like" environment that caused support beams to rust badly.
Ultimately, a weld subject to years of corrosion finally snapped, sending one vehicle and concrete crashing into the mall below.
The bodies of Lucie Aylwin, 37, and Doloris Perizzolo, 74, were pulled from the rubble a few days after the collapse.
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