Australia's workplace watchdog has sunk its teeth into a remote Northern Territory homestead, after it "chose to short-change" more than a dozen backpackers.

Key points: Legal action taken after 17 employees underpaid between $623 to $3,763

Legal action taken after 17 employees underpaid between $623 to $3,763 Operators of the Barkly Homestead fined a total of $56,766

Operators of the Barkly Homestead fined a total of $56,766 Fair Work Ombudsman said company "ignored advice" and "chose to short-change" employees

David Mayne Pty Ltd, which trades as the Barkly Homestead, has been fined $48,320 after admitting to underpaying 17 employees more than $23,000.

Homestead manager and company shareholder Andrew Mayne was also penalised $8,446.

The Barkly Homestead offers accommodation, a restaurant and roadhouse on the Barkly Highway, about 210 kilometres east of Tennant Creek.

Fair Work Ombudsman inspectors found David Mayne Pty Ltd paid more than a dozen workers a flat rate of $19.21 between October 2015 and April 2016, leading to a "significant" underpayment of their weekday overtime rates.

The workers were employed full-time, mostly as cleaners and waiters, and most were overseas workers in Australia on 417 working holiday visas.

The Fair Work Ombudsman said the company had obtained advice from an industrial relations specialist that detailed how it could go about lawfully paying employees an annualised salary, or pay employees the prescribed penalty and overtime rates.

It said the company ignored both options and instead "chose to short-change its employees for its own benefit".

Mr Mayne told the Federal Circuit Court in Alice Springs he had overlooked the company's obligations due to pressure of work in the business.

Most of the underpaid workers at Barkly Homestead were on 417 working holiday visas. ( ABC News: Emily Smith )

But Judge Tony Young said he "had some difficulty accepting that the breaches were the result of inadvertence."

"I consider that the underpayments were the result of at least recklessness … I am satisfied that there was a deliberate failure to inquire about and implement the provisions in the employee contracts … in relation to overtime rates," Judge Young said.

"A message needs to be given that these workers are as entitled to the same protection of minimum standards as an Australian worker."

Fair Work Ombudsman Natalie James said the outcome sent a message to employers.

"Ignoring advice about minimum lawful pay rates and short-changing employees' basic minimum entitlements is completely unacceptable conduct," Ms James said.

"Employers also risk facing enforcement action if we find significant compliance issues at their business and they cannot demonstrate that they have made a concerted effort to understand and comply."

The workers were back-paid in full last year, except for three who have not been located.

The Fair Work Ombudsman said it was holding the back-payments for those workers while it attempted to locate them.