Domino's Pizza workers are missing out on penalty rates worth at least $32 million a year due to an old deal struck between the company and the shop assistants' union.

Domino's is the latest large Australian company to come under scrutiny for controversial deals struck with the Shop, Distributive and Allied Employees Association (SDA).

A Fairfax Media investigation has uncovered that the union's agreements with Australia's three biggest employers – Coles, McDonald's and Woolworths – have resulted in hundreds of thousands of low-paid workers being denied penalty rates and higher casual loadings.

As a result, many of those workers are paid considerably less than the award – the basic wages safety net.