Midfield Meat's general manager Dean McKenna said on Friday that it looked like Warrnambool operation would close due to new government guidelines that cut their operations by a third.

He said management had been in discussions with various government departments and had their "fingers crossed that we can find a resolution to this massive problem for our region."

Mr McKenna told The Standard on Sunday that management was "still trying to reconfigure how we can operate the abattoirs going forward".

"We will not be working at full capacity because of the restrictions," he said.

"We will have a clearer idea on Monday morning and are still in discussions with the state departments."

A full shut down would see about 1000 Warrnambool people out of work for six weeks.

"The impact it would have on the local economy would be massive as it relates to around $10 million in wages," Mr McKenna said on Friday.

Premier Daniel Andrews said that under new COVID-19 rules, the city's largest employer would have to cut its operations by a third as region Victoria reverted to stage 3 restrictions.

The measure - that was placed on all of the state's abattoirs - would have meant cutting 340 jobs at Midfield Meat. The blow to the company's operations comes after it tested its entire workforce last month to ensure all workers were COVID-19 free.

Despite all workers testing negative after an infected inspector had visited the site, the abattoir was still being forced to scale back.