HORTICULTURE has lost out on a free trade agreement with South East Asian nations, exporters say.

And the deal has exposed a rift between horticultural exporters and the National Farmers' Federation, which has written to Trade Minister Simon Crean thanking him for the outcomes "on behalf of Australian agriculture".

Under the deal, Indonesia will place a 25 per cent tariff on Australian mandarins, onions and carrots until 2025 and 40 per cent on potatoes until 2020.

In the Philippines, carrots face a 40 per cent tariff; cauliflower, broccoli and lettuce 25 per cent; and celery 20 per cent, until 2020.

In Vietnam, a 20 per cent tariff on carrots and potatoes will be phased to zero by 2017 and a 15 per cent tariff on asparagus, celery and spinach will be removed by 2016.

The Department of Foreign Affairs and Trade claims major gains of the agreement, include the elimination of tariffs for oranges to Indonesia by 2010 and the Philippines by 2012 and the end of tariffs on grapes to Indonesia, Malaysia, the Philippines and Vietnam by 2018.

The DFAT claims the dairy, meat and wheat industries were the major winners from the deal.

But Australian Horticultural Exporters Association deputy chairman David Minnis said some tariffs were "unbelievably high" given the duties into Australia were zero.

"It makes it harder for us to get into the markets, horticulture loses out again," he said.

Mr Minnis also objected to the long timeframes for the phasing out of tariffs.

"They're extraordinary timeframes, it's just ridiculous, we'll be out of business by then," he said.

Mr Minnis said the NFF had "never shown any interest in horticulture, despite it being the second largest agricultural industry based on farm gate value".

AusVeg economist Ian James said vegetable growers would be "disappointed reductions aren't as rapid as they could be", although tariffs to Singapore and Malaysia would be removed quickly.

NFF economics and trade manager Charlie McElhone said the letter to Mr Crean's office was "not all about the outcomes of the deal".

"The intention is to acknowledge the efforts of the negotiating team; their transparency and liaison, which was first class," Mr McElhone said.

Mr Crean said the agreement was "very good news for Australian agriculture" and gave access to "almost 600 million people with a combined GDP of $US1 trillion".