Robert Taylor opened preliminary proceedings in the Burnie Magistrates Court as counsel for TT Line, the company which owns the Spirit of Tasmania and which has pleaded not guilty to charges over the deaths.

The company has been charged with one count of using a method of management reasonably likely to result in unreasonable and unjustifiable pain and suffering to the animal or animals in the group.

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It was further charged with 28 counts of a person transporting a horse across Bass Strait failing to ensure that the horse was individually stalled.

Presenting submissions to Magistrate Leanne Topfer ahead of evidence being heard, Mr Taylor said a "fair reading" of the legislation meant some of the charges can not be applied to the company.

Mr Taylor said a distinction must be made between the horses being loosely transported in the hold of the ship or, as they were, transported within a vehicle which was itself in the hold of the ship.

"None of these animals were loose in the hold of the Spirit of Tasmania," Mr Taylor said.

"They were contained in a vehicle."

Mr Taylor also said the regulations which inform the charges apply to a class of land-based vehicle such as trucks and trains, and therefore do not apply to a maritime vessel such as the Spirit of Tasmania.

The hearing continues Wednesday afternoon with submissions from Crown prosecutor Simon Nicholson, and lawyers for Andrew Williams and Thomas Martin who are also charged for the deaths.