A long-running industrial relations dispute at a Brisbane meat processing company ended on Friday with a result that would be laughable if it was not so devastating for 800 workers.

When the majority of employees at the Teys Australia Beenleigh plant voted in 2013 to accept a new Enterprise Bargaining Agreement that provided higher wages and annual bonuses, they could not have foreseen that their union – the Australasian Meat Industry Employees Union (AMIUE) would fight tooth and nail to oppose them.

Yet the AMIEU did just that, using the complexity of Australia’s industrial relations system to take the battle to the Federal Court, which ruled that while the Fair Work Commission made the wrong decision to back the union, it was legally entitled to make wrong decisions.

Friday’s final ruling means the EBA that provided higher wages and bonuses is void, and the employees revert to the 2010 EBA, costing most employees thousands of dollars each year.

Teys general manager corporate affairs Tom Maguire said the decision highlighted the failings of a broken IR system.

“This union has successfully fought to reduce the benefits of our employees, just so they can chest-thump and say they had a win,” he said.

In 2014 the new Teys’ EBA saw around 500 employees receive an average bonus of $4500. Similar bonuses for 2015 will now be lost, along with scheduled wage increases over the next two years.

The company has met with its workforce and explained that under the 2010 EBA, the current hourly rate will also decrease, meaning almost every worker will be worse off, some by around 12 per cent.

Mr Maguire said both the union and Fair Work Australia had completely failed Teys employees and the company, however committed to fix the problem and improve the conditions of its workers. He said a new plan to secure wage rises and bonuses would soon be announced.

“This result highlights the need for major reform.

“The actions of the union and decision of the FWC have shown the current IR system is incapable of securing the future for our workers. We have to find a better way.”