NFU Scotland is insisting that the current debate between governments in Westminster and Holyrood and the farming industry must include the move for animal health budgets to be placed under the control of the Scottish government.
It is unhappy with the Scottish government view that the agenda is being set and lead by Defra.
NFU Scotland believes that cost-sharing proposals by Defra in fact involve the dumping of costs upon the industry and could undermine agreements between industry and government in Scotland.
So it is calling for the control of animal health budgets to be given to the Scottish Government.
NFU Scotland president Jim McClaren, said: "Defra has been pushing the agenda of cost sharing for some time now.
"However, the reality as we see it is that it is simply trying to dump the costs of animals diseases onto an already struggling industry because of a tightening of its own budget.
"It is particularly galling to see such tactics so soon after the devastation resulting from the foot and mouth disease outbreak, the cause of which was a leak from a government-controlled laboratory."
McClaren added: "The relationship between industry and the Scottish Government works well and is highly valued.
"So the real debate here shouldn't be about cost-sharing but about how animal health budget, as well as animal health policy, can become the responsibility of the Scottish Government rather than Defra.
"We will also need to ensure that Scotland gets its fair share of the money."
He continued: "There hasn't even been a review of whether the costs Defra wants to dump on industry are either justified or proportionate and we simply cannot let their desire to dump costs undermine the good working relationship between industry and government north of the border."