Emanuel Exports and two of its directors have been charged over alleged animal cruelty following a deadly voyage from Fremantle to the Middle East.
Distressing footage showed thousands of heat-stressed sheep dying aboard the Awassi Express in August 2017, and the Perth-based live export company has since lost its licence.
In a statement on Wednesday, the West Australian Department of Primary Industries and Regional Development said charges had been laid under the state's Animal Welfare Act.
The charges relate to the "unnecessary harm caused or likely to be caused" to the sheep, of which 2400 died during the journey.
It comes after an 18-month investigation by compliance officers within the department.
The case will be heard in court at a later date.
"The company intends to vigorously defend the matter in court," Emanuel Exports managing director Nicholas Daws said in a statement.
"Emanuel Exports will make no further media comment pending the outcome of the hearing."
© AAP 2019