Horse industries have signed a deal with the New Zealand government to help protect them it from an outbreak of a costly equine disease.

The deal with the Equine Health Association formalises a partnership with the NZ government to improve biosecurity readiness and response, and means equine interests will have a direct say in managing biosecurity risk.

It's aimed at helping stop or deal with diseases like equine influenza, a 2007 outbreak of which is estimated to have cost the Australian horse industry more than $A100 million.

EHA chairman Ivan Bridge says a similar outbreak in New Zealand would almost certainly stop all movement of horses.

"Were this to occur midway through the year, it is probable all breeding would shut down. The cost would certainly run into tens of millions of dollars and potentially much more," he said.

"The importance of protecting our industry from disease incursions cannot be overstated."

Dr Bridge said New Zealand was now the only country in the world with a significant equine population where equine influenza has never occurred.

The Government-Industry Agreement Deed is the fourth the government has signed with a primary industry after pork, kiwifruit and pipfruit.