Partway through its forced relocation from Canberra to Armidale, interim Australian Pesticides and Veterinary Medicines Authority boss Chris Parker said on Thursday he had commissioned a "root cause" review of the agency's operational performance.

Citing "volatility" in performance measures and the agency's ability to meet legislative deadlines, Dr Parker said the probe will review delays in the agency's work, including assessment and registration of agricultural and veterinary chemical products and the issuing of permits.

The review will begin next month and be finished by the end of 2017.

The authority has seen an increasing number of applications, up by as many as 80 per quarter since the 2016-17 financial year - coming as staff departures reached nearly 20 per cent and recruitment of regulatory scientists to replace those walking out the door struggled.

In June, the Australian National Audit Office said the authority had failed to consider the risk staff would resign over its controversial move to Deputy Prime Minister Barnaby Joyce's New England electorate and was unprepared to manage the problem.

Almost a quarter, or 48, of the workforce resigned between July 2016 and February 2017, including 20 regulatory scientists, while the 57 staff who started were mostly non-ongoing, particularly in IT, case management and administration.

The authority has acknowledged "higher than normal rate of staff departures" and asked industry peak bodies for advice on how to be prioritise its assessment workload.

"Considerable work has gone into improving our systems and processes at the APVMA and we're not seeing this translate into more applications being assessed and finalised on time," Dr Parker said on Thursday.

"The performance audit completed by the Australian National Audit Office provided a view of how well the APVMA implemented the 2014 legislative reforms and gave an assessment on whether we'd achieved operational efficiencies, but this did not consider the wider impact or drivers of operational performance.

"We've got a unique opportunity here to look at our business more critically and build quality in our regulatory operations ahead of our relocation to Armidale."

He said the new review would give an objective assessment of what the authority could be doing better, through consideration of the drivers influencing operational performance.

"We're determined to improve our regulatory performance at the APVMA, and we will."

Former chief executive Karena Arthy walked from the job in April.

The June report said a drop in efficiency had been recorded since 2014 and the authority had not reduced the cost of regulatory burden on businesses seeking product approvals. Agency officials told senators in an estimates hearing in May it had struggled with a 15 per cent staff vacancy rate.

Its rate of departing staff reached 19 per cent in 2015-16, dwarfing the APS average of 7 per cent, as the Nationals promised Mr Joyce's New England electorate it would host the APVMA if it re-elected them at the 2016 federal poll.

Labor's agriculture spokesman Joel Fitzgibbon said Mr Joyce was guilty of a continuing "pork barrel joke".

"My advice to Barnaby Joyce's handpicked interim CEO is that he doesn't need to waste taxpayers' money on a review, he should just confront his boss about the mess he has caused," Mr Fitzgibbon said.

Mr Joyce, who faces a High Court challenge to his eligibility to sit in Parliament next week, and Nationals' deputy leader Fiona Nash are requiring all government ministers to justify the continued presence of public service departments and agencies in Canberra, Sydney and Melbourne as part of a whole-of-government decentralisation push.

Business cases for the next round of forced moves are expected by the end of the year.

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