The accusations were made during a court hearing packed with animal rights campaigners including the television screen writer, Carla Lane.
The Protesters Animal Information Network (Pain) argued that ferry operators were allowed, for commercial reasons, to sail in rough weather when vessel inspectors ought to be stopping them.
But Mr Justice Latham ruled: "In the light of the evidence it is not possible to conclude that [the Ministry of Agriculture] have put in place or are operating an unlawful policy."
Pain director Ms Lane said:"The fact is we did prove that animals went out in rough seas contrary to the rules. The minister, we feel, was responsible. But we could not actually prove that he had a policy of not intervening and stopping them."
Pain was attacking the activities of animal ferry operators based at Channel ports including Dover, Shoreham-by-Sea, West Sussex, and Brightlingsea, Essex. Its counsel, Richard Barton, argued that Mr Hogg was under a duty imposed by the 1994 Welfare of Animals during Transport Order to prevent "serious risk of injury, suffering or death" to animals bound for the Continent but had failed to issue the appropriate guidelines to inspectors, and they had failed to act.
He said in rough weather the chartered boats - smaller vessels than cross- Channel passenger ferries - rolled considerably, putting the animal cargoes at risk of injury.
Dismissing their application for judicial review, the judge ordered the protesters to pay the ministry's legal costs, estimated at about pounds 30,000.
Later Ms Lane said: "We are enraged. This evil trade appears to be protected and once again the people of this country have been ignored.
"We will fight on, not violently but certainly noisily."Reuse content