The Northern Territory Cattleman's Association (NTCA) has challenged federal Agriculture Minister Murray Watt's support for his government's decision to phase-out the live sheep export trade.

In Darwin today, NTCA president David Connolly told the organisation's annual conference that he did not think Mr Watt, who was in attendance, supported the shutdown of the live sheep trade.

"Both Minister Watt and I have a boss that pays our salary that feeds our family," Mr Connolly said.

"When my boss says, 'Go chop the wood', I go chop the wood.

The Labor Party has committed to ending the live sheep trade, but has promised not to touch the live cattle trade.

Mr Connolly said while he believed Mr Watt's assurances that the live cattle trade was safe, northern cattle producers were still concerned.

"If the minister's boss says, 'Go close the cattle trade', what do you think will happen then?" Mr Connolly said.

'The right thing to do'

Minister Watt defended his government's policy and said he did support the shutdown of live sheep exports.

"I think that it is the right thing to do," he said.

"I do think there are significant differences between the live cattle industry and the live sheep, and it's not just me — our whole government, from the prime minister down, believes that."

Minister Watt said the mortality rates for live sheep exports, compared with live cattle exports, were markedly different.

"I think the other big difference is the economic contribution that both of these industries make," he said.

"It's not the only factor to consider — the animal welfare issues, the loss of social licence — are factors as well, but we can't ignore the fact that the live cattle industry is a key economic industry in northern Australia.

"The reality is that live sheep exports actually plummeted under the former government, the coalition government, by 70 per cent and they now represent less than one per cent of Western Australia's agricultural exports."

This month, NTCA was part of a group of 25 agricultural industry groups from across Australia which sent a letter to Minister Watt saying the sheep ban "represents a red line that cannot be crossed".

Mr Connolly said cattle producers in northern Australia were still worried that the live cattle trade was under threat.

"For us it is an unimpeachable truth, that losing the live sheep trade will do nothing but empower those, who do not just oppose live export, but livestock farming in general," he said.

"Which industry is next? Cattle, pigs, chickens, or will we see fertiliser and glyphosate banned as in Europe?"