Thousands of employees across Australia are unknowingly trapped in so called "zombie" workplace contracts created during the WorkChoices era, an ABC investigation has found.

One of South Australia's largest employers, On The Run, has chosen to finally phase out WorkChoices-era contracts for over 3,000 of their employees, offering them the full workplace privileges they are entitled to.

But lawyers and unions say tens of thousands of other Australian employees across the country remain unaware that they are stuck in WorkChoice era agreements, largely due to a loophole in the modern industrial relations system that the Federal Government has so far refused to close.