The Perth-based company lost its licence after distressing footage was broadcast showing the sheep dead and dying from heat stress aboard the Awassi Express in August 2017.

In July, Western Australia's Department of Primary Industries and Regional Development laid charges under the state's Animal Welfare Act.

Former managing director Graham Daws, whose son Nicholas has since taken over the role, and ex-director Michael Stanton did not appear in Fremantle Magistrates Court in person on Friday.

But defence counsel Genevieve Cleary said they and the company would very likely plead not guilty at a future court date.

By agreement with the prosecutors, the matter was adjourned for further discussions and legal advice, and moved to Perth Magistrates Court for a mention only on November 15.

"I seriously doubt there will be a plea of guilty," Ms Cleary said, estimating a trial would last at least one week.

Outside court, Animal Justice Party spokeswoman Virginia Thomas-Wurth said it was disappointing the company and the two former directors faced only 16 charges each given so many animals had died.

"We are going to turn up to bear witness to this trial whenever it does happen," she told reporters.

"I think a message needs to be sent that the community does not tolerate animal abuse and we'd like to see it prosecuted fully."

Mr Daws vowed, swiftly after the charges were laid, that the company would vigorously defend itself.

The charges came after an 18-month investigation by compliance officers within the department.

Australian Associated Press