The Federal Government and horse industry have finally agreed how to fund future disease outbreaks, like horse flu.

The 2007 outbreak of horse flu cost taxpayers millions of dollars, and governments and industry have struggled to reach agreement on cost-sharing ever since.

But last year, governments said they wouldn't pay for another outbreak unless the industry signed the Emergency Animal Disease Response Agreement.

Yesterday in Canberra, the peak horse bodies signed the deed.

The agreement means that the Australian Government will pay for all costs associated with a disease outbreak, but then the industry has ten years to pay its share of the costs.

The horse industry had previously disagreed how to collect its funding share.

Recreational horse owners had concerns that a compulsory levy would disadvantage them, but now the industry has agreed to place a levy of about 50 cents on manufactured feed and wormers.

But it seems like it's not all over yet.

The Stock Feed Manufacturers' Council of Australia's John Spragg says his members don't want a levy on feeds.

The Australian Campdrafting Assocation says the levy, though not ideal, is necessary.

President Sean Dillon says his sport was greatly affected by the quarantining of horses during the 2007 horse flu outbreak, and he's still not happy with national quarantine regulations.

"I've got grave concerns over the continued operation of quarantine at a government level and even if you put all of that aside and forget that, just the huge volume of horses that still move intercontinental."

The EADRA is administered by Animal Health Australia, and CEO Dr Mike Bond says he realises that there's still some work to be done.

"These arrangements are going to be reviewed in five years time," he said.

"So that's going to give us five years to consider other possible levy mechanisms and so that's going to be enshrined in any legislation that's put in place, so it's not there forever and a day."

The horse industry is the last of 11 livestock groups to sign up to the EADRA.

Story: www.abc.net.au