A workplace deal that would have forced Kmart employees to pay their super into underperforming industry fund REST would have left them worse off than their industry award, the Fair Work Commission has ruled.

The commission on Monday struck down a deal negotiated between the department store and the main union representing its workers, the Shop, Distributive and Allied Employees Association (SDA) over issues to do with the voting process.

In an unusual move, commission deputy president Amanda Mansini flagged that even if the voting problems had not occurred she was not convinced workers would have been better off under the deal, which would take away the benefit of choosing a fund.

Workplace deals need to leave workers better off overall compared to the relevant award. This so-called BOOT test has become controversial after a landmark decision involving Coles found all workers, not just a selection, had to be better off.