The owners of a Northcote cafe investigated for underpaying employees have reached a settlement with a former staff member over her wrongful termination.

The settlement came hours before the former Barry cafe employee, Anna Langford, was to file an official wrongful termination complaint in court.

The Fair Work Ombudsman opened an investigation into Barry cafe earlier this year, following complaints from current and former staff who said they were being underpaid by at least $5 an hour.

A number of workers, including Ms Langford, said shifts were cancelled after the complaints about underpayment were made.

In a letter to Ms Langford, the cafe's owners said they "deeply regret the circumstances" that led to her "wrongful termination".

"If we could have our time again, knowing what we now know, we would approach things very differently," they said.

"We accept that we cannot change our past mistakes, and we apologise for the distress that our actions caused to you and your co-workers.

"We intend to remedy the underpayments to staff and have undertaken steps to do so."

Anna Langford says she was fired after raising concerns about underpayment. ( Supplied: Anna Langford )

Ms Langford said she was pleased the cafe's owners had changed their tune, and said the apology was "really significant".

"It's different to what they originally said," she told ABC Radio Melbourne.

"I'm just really happy that this has come about, because it will show a lot of young workers that we can win in cases like this.

"So many people across the [hospitality] industry are too afraid to to speak up and stand up to exploitative bosses."

The cafe said it had sought "specialist advice about the correct pay rates and conditions", and would "use this day to settle the dispute, draw a line in the sand and move forward".

