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The Queenstown Lakes District Council has filed charges under the Building Act against both Dominion Construction Ltd, and one of its former employees.
They are charged with cutting starter bars at the pre-cast concrete to wall foundation junctions at Block A of the Kmart building, on or before August 2.
If found guilty, they face a fine of up to $200,000 each.
A Dominion Construction spokeswoman said the company would not be making any comment while the matter was before the courts.
Council spokesman Naell Crosby-Roe confirmed the charges had been laid, but said the council could not comment further while they were going through the court process.
The Kmart building is part of the first stage of the $100million Queenstown Central development in Frankton.
The opening of the building was delayed by construction problems, with a "Notice to Fix" issued by the council in late August.
It finally opened its doors on October 18, two weeks after it was supposed to.
A first appearance in the Queenstown District Court is scheduled for March 25.