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.

Josh Cullinan, a tertiary education union official whose analysis of the wage deal identified that younger workers would be hardest-hit, said Fair Work's decision was "remarkable".

"It is a positive outcome that the intervention of the broader community has seen casual staff secure 5 per cent more pay and junior workers paid more," Mr Cullinan said.

"Never before have so many low paid workers benefited from the intervention of the broader community in spite of a deal done by an employer and a so-called union."

The Fair Work Commission's decision will embarrass the Shop, Distributive and Allied Employees Association, confirming the union negotiated a deal that would have underpaid many thousands of workers.

Coles operations director Andy Coleman said the new Store Team Agreement would deliver increased benefits including a 3 per cent basic wage rise to more than 75,000 staff.

He said Coles had been happy to accommodate the changes requested by the Fair Work Commission.

The agreement also includes extra support for families, including five days' compassionate leave and a newly introduced leave entitlement for domestic violence victims, Mr Coleman said.