Hundreds of Australia's lowest-paid workers have been ripped off by two childcare centre operators in Melbourne and Perth.

An investigation by the federal workplace watchdog has discovered that 114 minimum wage-earning childcare workers at Melbourne's Wonderkindy centres were denied award-rate pay and entitlements, short-changing them by almost $140,000.

A West Australian chain of childcare centres has also been put on notice after the Fair Work Ombudsman found it underpaid 160 childcare, cleaning and kitchen staff.

Wonderkindy operated its Melbourne childcare centres at Tullamarine and Port Melbourne, the latter of which was recently ranked the worst childcare centre in Victoria in a federal government report.

Company director Allan Coman has been ordered to pay back-pay and issue formal apologies to workers. His company has recently closed down and is in the process of being sold.

But Australian Securities and Investments Commission documents show Mr Coman controls another company running the Wonder Child Care Centre in Avondale Heights, which is still trading.

Former Wonderkindy staff have spoken out about the company's dishonest practices and raised concerns that Mr Coman remains active in the childcare sector.

An former employee at the Port Melbourne centre, Sarah Goodson, 30, is owed more than $3000. She said wages were never paid on time and rarely made in full.

"I would call him and say; 'you owe me money, and I can't  pay my rent' ... but he didn't care," Ms Goodson said.

"Parents were paying for a more expensive service, getting charged $105 a day, but the kids were just getting looked after and that's it – they weren't getting taught anything. There was no painting, no creative activities. There was never any money. Even staff were having to buy things for the centre out of their own pockets."

Gayle Fitzpatrick, who was not paid superannuation or overtime hours, said dozens of disgruntled staff had been pursuing Mr Coman for money owed for years.

In a letter to employees, Mr Coman admits breaching workplace laws and expresses "sincere regret".

He has signed an agreement with the Ombudsman to comply with the law if he continued or resumed trading after the transfer of business. Mr Coman could not be reached for comment.

Wonderkindy Port Melbourne was ranked one of the 12 worst childcare centres out of 1400 nationally in a report by the Australian Children's Education and Care Quality Authority. It was the only Victorian centre in the "significant improvement required" category.

Childcare union United Voice said childcare was a skilled profession but employees made about the same wage as a supermarket cashier.

Early Childhood Australia chief executive Samantha Page said underpayments were disappointing given childcare staff were "some of the lowest-paid workers doing some of the most important work".

Fair Work Ombudsman Natalie James said misunderstanding workplace obligations could result in a "hefty bill" for back-payment, "so it is important employers get it right in the first place''.