A Coles supermarket worker has won the first round of a David and Goliath battle which exposes a major union to claims it sold out its own workers.

Duncan Hart, a student who works part time at a Coles supermarket in Brisbane, took action in the Fair Work Commission claiming that the enterprise bargaining agreement between Coles and his union, the Shop Distributive and Allied Employees Association (SDA), left thousands of workers worse off.

In a decision published on Tuesday, the Fair Work Commission granted Mr Hart the right to appeal the approval of the EBA, saying there was an argument to be made the deal failed what is known as the 'better off overall test' (BOOT).

For a workplace agreement to be legal, all employees must be made better off when an agreement is compared to the award.

The Coles agreement in question, which was approved by the Fair Work Commission in July, mandates a higher hourly base rate for supermarket workers, but cuts penalty rates for weekends and nights.

Mr Hart argued this left a substantial proportion of Coles' workforce worse off than if they were paid under the existing award.

In their decision, the commissioners said the agreement should be further tested to ensure it passed the BOOT for all of the 77,507 Coles and Bi-Lo workers covered by the deal.

"We are of the view that confidence in the agreement approval process would be enhanced if all the material intended to be relied upon by Mr Hart is considered," the commissioners wrote.

"We propose to grant permission to appeal and allow parties to lead such additional evidence as they see fit."

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Mr Hart, 23, said he hoped the decision was the first step towards increasing the wages of low-paid Coles workers.

"It's absolutely fantastic, it's exactly what I hoped for," Mr Hart said.

"It's good that this gives us the avenue to get justice. Now Coles and the SDA have to deal with the substance of the argument, instead of trying to dismiss our claims without considering the figures we've put forward."

Mr Hart's appeal was based largely on research by Joshua Cullinan, who is an official in the National Tertiary Education Union but undertook the analysis in a personal capacity.

Using a small sample of rosters provided to him by Coles, Mr Cullinan calculated two-thirds of permanent employees at two Coles stores in Victoria would be financially worse off by an annual total of $55,000. He then extrapolated this across 770 Coles stores Australia-wide.

The Commission will now put Mr Cullinan's calculations to the test at an additional hearing before deciding on whether or not to accept Mr Hart's appeal.

At a hearing before the commission earlier this month, Coles argued that the commission should reject Mr Hart's appeal because Mr Cullinan was the real appellant and was not made worse off by the workplace agreement.

However, the commissioners rejected this argument and ruled that Mr Hart had a right to appeal.

A spokesperson for Coles said it was proud of the agreement which it said increased the base rate for its employees by an average of 3 per cent a year.

"That's well ahead of inflation and a very positive outcome for our team who overwhelmingly endorsed the agreement," the spokesperson said.

"We believe it is a good agreement for our team, and we will be making that case very strongly to the Commission."

The SDA has been contacted for comment.