The agency has been in upheaval over the past two years after then agriculture minister Barnaby Joyce ordered its move from Canberra to Armidale.

Chris Parker was appointed in November 2017 and has led the controversial move, which was completed in July this year.

The shift saw an exodus in staff with indications staff quit rather than move to the new country headquarters, a nine-hour drive from Canberra.

Over the 12 months to June, 86 people were recruited, which suggests that half the agency's current head count of 171 are relatively new.

Dr Parker said he was resigning for personal reasons and would remain as chief executive until a replacement could be found.

His job has been advertised, with applications closing on January 12. The advertisement says the position "will be permanently based in Armidale, with the successful applicant expected to initially spend a reducing proportion of their time in Canberra as the relocation progresses".

Just 14 staff relocated to Armidale in the 12 months to June 30 this year, according to the agency's annual report. Forty-two staff took voluntary redundancy on July 1. Fifty-one staff remain in Canberra.

Dr Parker's resignation continues the turmoil in the agency. Former chief executive Kareena Arthy quit as the move to Armidale began in early 2017. She took up a job with the ACT government. Dr Parker is on leave and has not said what he will do.

The agency's annual report suggests a big increase in the travel bill in the past two years coinciding with the move to Armidale. In each of the previous two financial years, the agency spent just short of $200,000 on travel. In 2017-18 it spent $480,000, and in 2018-19 it spent $625,000.

Labor's Joel Fitzgibbon told parliament recently he had seen Dr Parker regularly at the airport.

"He was going to be located in Armidale, we were assured of that. He probably does have a house or a flat or duplex in Armidale I suspect. But I see him flying to Canberra a lot," Mr Fitzgibbon said.

The agency is set for a renewed focus again in January when the coroner reviews evidence about a suspicious fire at the site of the new office in Armidale.

A suspicious fire razed the Armidale Club, which operated from the site. The fire, which a previous coroner's report found was deliberately lit, came as the government was looking for a site to build its new office.

The previous coroner came to no conclusions about who was responsible. After the site was chosen for the APVMA and amid agitating from the Armidale Club owner, who lost her business, police reopened investigations a year ago. The NSW coroner is to review evidence in January.