In the case before the Darwin Magistrates Court, Keith Simpson Transport Operations has been charged with three counts of animal cruelty but pleaded not guilty to the charges.
Territory's Animal Welfare Authority says the goats were brought from Bourke in New South Wales for the Territory in July last year.
The authority says the goats, which are bound to live export market, were not given enough food or water. Prosecutors are expected to say 300 goats died as a result.