Supermarket giant Coles has admitted underpaying much of its workforce in cosy deals it struck with the conservative shop assistants union.

For two years, Coles has tried to deflect from the findings of a Fairfax Media investigation that revealed massive underpayment at the supermarket.

Up to 60 per cent of Coles workers would be better off if they were paid minimum award rates, the Fair Work Commission has heard. Credit:Robert Rough

But in the Fair Work Commission on Thursday its lawyer, Stuart Wood, QC, indicated that much of the Coles workforce - up to 60 per cent - would be better off if they were paid minimum award rates rather than what they are paid from deals struck with the Shop, Distributive & Allied Employees Association (SDA).

The admission comes as Coles tries to fight off a huge back-pay claim for tens of thousands of its workers from Brisbane night-fill worker Penny Vickers.