The Otago programme manager, Joe Bayley, and his Southland counterpart, Dave Burgess, were both overlooked for the new position, created when the Southland, Otago and South Canterbury regions were combined into one entity.
Some farmers feel the experience of Mr Bayley and Mr Burgess, with a combined knowledge of more than 50 years in the war against bovine tuberculosis, was something that should be retained.
The successful applicant was Brent Rohloff, who currently works for Mr Bayley's pest control company, Southern Pest Management.
He will oversee control of vectors from his Dunedin base, covering the area from the Rangitata River to Bluff.
Farming leaders, who asked not to be identified, said they had confidence and would support Mr Rohloff, but believed the two senior candidates were better equipped for the job, but were not appointed by the Wellington-based Animal Health Board because of a possible personality clash.
One leader described Mr Bayley as not a "system's man", and someone who would challenge Wellington bureaucracy in order to get the job done.
The three southern TBfree New Zealand committees support the move to rationalise vector management, but they told the AHB of their concerns at the loss of experience for a $10 million vector control operation which will now cover 3.3 million ha.
Farming leaders in Otago spoken to say Mr Bayley's achievements spoke for themselves, and they credit him for reversing what was the worst Tb infection problem in the country.
In 1997, when Southern Pest Management was appointed to control bovine Tb vectors in Otago, the province had 280 infected herds but, with some herds becoming disease free and others becoming infected, there were 100 new infected herds a year.
Today, there are 24 infected herds in the southern South Island, of which 18 are in Otago.
Sources say Mr Bayley and his business partner Ron Walker related well to farmers, landowners and interest groups, and were able to secure access to properties and calm tensions.
One farmer said Mr Bayley's skills eased potential conflict with hunters in the Blue Mountains and Waianakarua, where possum control operations were proposed.
Compare that with conflict and tension with vector control operations on the West Coast, he said.
The farmer said Mr Bayley talked and listened to opponents and, in the case of Waianakarua, lobbied the Department of Conservation to get a trial of deer repellent possum bait which helped eased hunter concern but allowed the poison programme to proceed.
The new, enlarged programme would be challenging and came at a critical time in the war on Tb.
It would move from a broad-brush approach of killing every possum to a more targeted approach of finding incidents of the disease and killing possums in that area.
While sources say Mr Rohloff can do the job, they say Mr Bayley's expertise would have been invaluable.
Animal Health Board chief executive William McCook said in an interview that a potential clash of personalities was not a reason for Mr Bayley being overlooked.
He said in an interview the board ran an open recruitment process and the best person was appointed to the job.
While mindful of the need to keep momentum with the southern South Island programme, Mr McCook said he also wanted a blend of knowledge, skill and expertise, along with new ideas and ways to do things.
Mr Rohloff will head about six staff, including a planner, community relations manager, field staff and contract administrators.
He would report to a vector operations manager in Wellington. Nationally, there were 11 vector managers.
Graham Clarke, a former chairman of the Otago Regional Animal Health Committee, now known as the Otago TBfree committee, was sad to hear Mr Bayley had been overlooked for the job, saying deer and cattle farmers had much to thank him for.
"Otago dropped from an appalling position to a relatively good position much faster than theoretically possible, [and] that was because of the quality of vector control Southern Pest Management oversaw."
The company got residual trap rates - the number of possums that survived poisoning - down to 1% through good practices, compared to 5% in the North Island, an achievement Mr Clarke said ultimately saved farmers money and importantly reduced infection rates.