Three of Australia's largest coal mining companies will fight the government's multi-employer bargaining policy in the Federal Court, in a case that could have a significant impact on thousands of Australian workers.

Whitehaven Coal, Peabody and Glencore subsidiary Ulan Coal Mines have lodged an appeal in the Federal Court against a Fair Work Commission decision that required them to engage in multi-employer bargaining.

The commission's August ruling found the operators of three New South Wales underground black coal mines satisfied the requirements for a single interest employer authorisation due to common interests.

The Association of Professional Engineers, Scientist and Managers made the application for multi-employer bargaining, a change the companies have described as "dangerous" and "punitive".

It's a major test for the Albanese government's industrial relations changes, which allow employees from different workplaces with similar interests to be covered under one enterprise bargaining agreement.

Earlier this month, the Minerals Council's chief executive Tania Constable warned the laws were bringing conflict "to every workplace".

Peabody's chief executive Jim Grech said the company was "confounded by the federal government's continued attacks", prompting it to join with the other operators to apply to have it set aside.

"This dangerous precedent undermines our ability to fairly negotiate employment terms and conditions with our employees at Wambo or any of our other operations," he said.

"The decision also extends beyond the three companies involved, potentially dragging entire sectors into lengthy and complex multi-employer negotiations, and erodes Australia's competitiveness by stripping companies and employees of their right to directly negotiate workplace conditions."

Glencore warned Australia risked a return to the "dark days of the 1970s and 1980s" with an increase in industrial disputes as a result of the government's laws.

"Forcing business competitors to engage in collective bargaining creates more uncertainty, undermines business confidence and future investment, reduces productivity and will ultimately lead to more industrial disputes," the company said in a statement.

Whitehaven Coal warned multi-employer bargaining would put jobs and investment at risk and fuel inflation.

"Enterprise-level bargaining has proven to be a successful framework for several decades, enabling employers and employees in the mining industry to negotiate workplace-specific outcomes that recognise the differences that exist between competing companies and operations," the statement read.

Speaking at the National Press Club last week, Employment and Workplace Relations Minister Murray Watt disputed claims of industrial action risks, saying action had decreased recently.

"For all the people out there talking about workplaces full of conflict, the facts don't back it up," Senator Watt said.

"It is not wreaking the havoc that people are arguing.

"We have had one single interest multi-employer agreement reached since the law was changed in an industry that probably most people have had no experience of whatsoever, heating, ventilation and air conditioning."

The bargaining changes, which took effect in June last year, require the Fair Work Commission to issue an authorisation before negotiations can start.

To be eligible, at least some of the employees to be covered must be represented by a union.