The agency that former deputy prime minister Barnaby Joyce demanded move to his own electorate has been forced to maintain a Canberra office amid fears staff departures would risk its ability to do its job.

The chemical and pesticides regulator, Australian Pesticides and Veterinary Medicines Authority (APVMA), will allow about a quarter of its staff to keep working from its Canberra office, while the remainder will work from Armidale in regional NSW.

There has been a high turnover of staff, including the departure of the former chief executive, since Mr Joyce announced the move during the 2016 election.

APVMA chief executive Chris Parker said between 30 and 40 staff would remain in Canberra, including specialist scientists and "decision makers".

"Our existing plans for teleworking, an enhanced reliance on external scientific assessors and recruitment into Armidale have not reduced our relocation risks to an acceptable level and more must be done," Dr Parker said.

"Retaining the knowledge and expertise of our scientists is essential to the effective operations of the APVMA and accommodating these staff in a Canberra office further supports the APVMA to deliver its statutory obligations."

During the last federal election, then-deputy prime minister Barnaby Joyce announced the APVMA would shift to Armidale, which is within his New England electorate.

The authority had 198 staff at the end of June 2016, but since then at least 110 of its employees have departed, including 33 regulatory scientists.

Earlier this year, Dr Parker told Senate estimates the APVMA had recruited new staff since the departures and expected "core business" to between 170 and 180 workers.

During that appearance he was adamant that not all staff would be in Armidale.

Expensive proposition 'would have fallen short'

More than 20 APVMA are already working from an interim office in Armidale while the new building to house the APVMA is being constructed.

Dr Parker said he had advised Agriculture Minister David Littleproud, who took over the portfolio last year, of his decision to retain the Canberra office.

"We've had a number of risk mitigation strategies in place to ensure that we maintain the performance of the organisation," Dr Parker said.

"I think from the intentions survey that we undertook earlier this year we found that, as expected, a large number of staff did not want to move to Armidale."

A Senate Estimates hearing last month was told the internal survey process showed 70 per cent of staff did not wish to relocate.

A separate estimates hearing last year revealed a number of staff had been working from the Armidale McDonalds fast food restaurant due to a lack of office space.

Dr Parker said the authority looked at whether staff could work full-time through tele-working, but deemed it an expensive proposition that would not have met the "organisation's need".

The organisation also attempted to find external workforce option through an expression of interest.

"Really that has not delivered what we were hoping out of that, there are some gaps, and it's really not a viable option for us," he said.

Labor demands full reversal

Shadow agriculture minister Joel Fitzgibbon said the relocation plan was a "flop" and should be ditched completely.

"The Turnbull Government is gradually running up the white flag on its crazy forced relocation," he said.

"The blatant pork-barrelling exercise has been a flop and only a complete backflip from the Turnbull Government will deliver the capacity our farmers and other key stakeholders need."

Mr Fitzgibbon has persistently criticised the cost of relocation, and is now questioning whether those expenses could end up being passed on.

"Speculation is rife that there is more bad news to come, including increased approvals charges for those who manufacture the pesticides and veterinary products," he said.

Dr Parker said he had recently signed a lease on a second interim office, which would accommodate an extra 32 staff in Armidale.

Its purpose-built offices are expected to be finished by the middle of 2019 and would house about 150 staff.

Once the Canberra office is reduced to about 40 staff, the APVMA will assess sub-letting options.