The government agency Barnaby Joyce pushed from Canberra into his own electorate has lost more than half of its workforce in under two years, new figures reveal.

And only a quarter of staff currently with the beleaguered pesticides regulator say they are likely to move to Armidale.

"This has negative impacts in terms of the agriculture industry, in terms of the services the APVMA can provide, and that's problematic for everybody," the public sector union's Brooke Muscat-Bentley said.

The Australian Pesticides and Veterinary Medicines Authority (APVMA) assesses agricultural and horticultural chemicals before they can be used in Australia, including products used by households.

During the 2016 election campaign, the former deputy prime minister announced the APVMA would be relocated to the New South Wales regional town.

The authority had 198 staff at the end of June 2016.

Since then, at least 110 of its employees have departed, including 33 regulatory scientists.

"I don't think it's a disaster," APVMA chief executive Chris Parker said of the staff exodus.

"We had more staff leave than would normally leave … for an organisation of this size.

"It's a challenge, of course it's a challenge [but] we've put a whole range of things in place to maintain the knowledge that we have."

Staff have 'very good' reasons not to move

The agency said it had filled nearly all of the vacancies — but the majority of the replacements do not intend to shift to Armidale.

The Australian Pesticides and Veterinary Medicines Authority in Canberra. ( ABC News: Ian Cutmore )

A recent survey showed 37 staff were 'likely' or 'very likely' to relocate.

They would join two employees who have already made the 750-kilometre move, and another who is currently relocating.

"People actually had very, very good reasons for [not moving]," former APVMA regulatory scientist Ron Marks said.

"Looking after older parents, children going to college, medical reasons, in some cases shared custody, where you couldn't go more than 50 kilometres from Canberra."

Mr Joyce last night insisted the relocation would be, "a great outcome for our nation in the medium to longer term".

"You've always got to make hard decisions, you've always got to iron them out, and that's precisely what we're doing now," Mr Joyce said.

More money offered to relocate amid difficulties

Along with bleeding staff, a raft of other difficulties have faced the small regulatory authority ahead of its move next year.

Documents obtained by the ABC under Freedom of Information show:

Construction of its new headquarters in the northern New South Wales town is weeks behind schedule.

Construction of its new headquarters in the northern New South Wales town is weeks behind schedule. Staff rejected a $30,000 relocation offer as inadequate, fearing they would be left out of pocket.

Staff rejected a $30,000 relocation offer as inadequate, fearing they would be left out of pocket. There is a high risk customers will lose confidence in the APVMA, and it will be unable to attract suitable candidates for key roles.

"This has been a mess from the outset," Ms Muscat-Bentley said.

"A decision has been made on a political whim to uproot all these people … this is something that should never happen again."

The agency is now offering reimbursement of up to $55,000 to those who relocate, along with retention bonuses worth thousands of dollars.

Labor's agriculture spokesman Joel Fitzgibbon yesterday used Parliament to demand documents relating to the APVMA's digital strategy.

He argued part of that plan would investigate ways for staff who still refuse to move to Armidale to work remotely.

"It's an admission of failure," Mr Fitzgibbon said.

"How do we say we've relocated this thing to Armidale, while at the same time keeping the people we really need here in Canberra?

"It's a fraud, really, on the people of Armidale and the electorate of New England."

Delays may leave farmers without products

The high-level documents reveal officials expected construction of its new headquarters to begin this month.

But the successful tenderer was announced months later than expected, and work is now tipped to begin in the middle of the year.

"We anticipate, certainly given the contract we've signed, that'll be finished for us to move in on July 1 [2019]," Dr Parker said.

APVMA chief executive Chris Parker. ( ABC Regional: Brett Worthington )

The agency's compliance work, along with some legal, payroll, and human resources functions, could be outsourced to other departments or the private sector, the documents show.

And the agency will need to use external providers, "for the bulk of its scientific assessments", an external consultancy firm concluded.

During the 2016-17 financial year, 69 per cent of the APVMA's product assessments were finalised within statutory timeframes.

Dr Parker said the agency had seen a "significant improvement" in on-time performance during the three months from October to December.

Delays in approving products can cost companies hundreds of thousands of dollars, and can leave Australian farmers without products their overseas rivals are using.

Ron Marks, who spent two decades at the APVMA before retiring last year, acknowledged the agency was trying to mitigate the damage caused by the move.

But if things went wrong, he said, "timeframes could lag for some years".