The Australian Competition and Consumer Commission (ACCC) claims VW intentionally sold more than 57,000 such vehicles over a five-year period.
It is seeking a public declaration of misconduct, financial penalties and corrective advertising.
VW Australia said it is reviewing the ACCC claims.
In a statement, the company said it does not think that the court action “provides any practical benefit to consumers because software solutions for cars affected by the voluntary recall are expected soon”.
Volkswagen Group Australia managing director Michael Bartsch said: “The best outcome for customers whose vehicle is affected is to have the voluntary recall service updates installed.”
The ACCC lawsuit covers 10 VW car models including the top-selling Golf, Passat and Polo,
ACCC chairman Rod Sims said in a statement: “These allegations involve extraordinary conduct of a serious and deliberate nature by a global corporation.
“We expect higher standards of behavior from all companies that supply to Australian consumers.”
The world’s second-biggest auto maker is also facing several private class action lawsuits in Australia.
VW has suffered a global backlash since revealing last year that around 11 million of its vehicles had software or so-called “defeat devices” designed to bypass official emissions tests.
The company has since had to pay billions of dollars in fines and settlements with both regulators and customers around the world.
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