Supermarket giant Coles will have to pay millions of dollars more in casual and junior staff wages after Australia's industrial umpire intervened in a deal covering 75,000 workers.

The Fair Work Commission has sought changes to the three-year workplace agreement struck between Coles and the conservative shop assistants union, which had been criticised as a sweetheart deal.

First revealed by Fairfax Media, major flaws in Coles' proposed nationwide deal meant thousands of low-income workers would not be "better off overall" compared to the retail industry award, the basic wages safety net.

The Fair Work Commission ruled on Friday that the Coles deal must increase casual loading from 20 to 25 per cent. Thousands of casual staff will secure 5 per cent pay rises and junior workers aged 19 or under will receive higher rates.

Workers aged 17 will receive 60 per cent of the adult pay rate, while 18-year-olds will receive 70 per cent.