Tri NZ will receive $750,000 from the taxpayer this year, a figure which has gradually dwindled from $1.4 million in 2014.
Elliott's exit coincides with a revolution of reviews into cycling, football, hockey, rowing, netball and triathlon as the country grapples with how to find the right balance between the pursuit of medals and athlete wellbeing.
NZME's efforts to contact Elliott were unsuccessful. He will leave by the end of the month.
Tri NZ chief executive Claire Beard said, via emailed answers, that any employee was entitled to make such a call.
"Mark resigned, and we gave commentary and context around that in a media statement.
"There is no place for robust discussion around an employee's decision or any reason to link that to taxpayer funding of a sport."
Pilone has mentored other high profile triathletes such as Andrea Hewitt and Ryan Sissons in recent years. Sissons clashed with Elliott and the governing body in July after his exclusion from the mixed team relay world championships.
"I found Mark's conduct not up to my standards, and not what I would expect of a person in that position," Pilone said.
"I have no knowledge of any recent events that may have brought about Mark's departure, but it could be a symptom of wider problems within that organisation."
Beard said an appeal process was available to contest decisions.
"Triathlon New Zealand has an independent panel that is involved in all steps of the selection and nomination process. There are also robust policies to support all selections.
"As an organisation we strive to improve, and have recently put in place a policy development panel that includes both athlete and coach representation.
"This group have been tasked with supporting the development of the Tokyo 2020 nomination policy."
Pilone said his recent dealings with Elliott differed markedly with previous experiences, like when their respective athletes - Carter under Pilone and Bevan Docherty under Elliott - duelled against each other on the hills of Athens 14 years ago.
"Prior to the first four months of this year I had a very high opinion of Mark both as a person and also in his role as high performance director for various sports in New Zealand over a number of years."
Pilone stressed the issue was wider than just one person or one organisation.
"In New Zealand, the only measure of success we have for the high performance programmes of the various Olympic sports appears to be medals at major championships.
"This has the potential to place both staff and athletes within those programmes under tremendous pressure. On occasion these people may act in a way that they normally wouldn't with irrational decisions, looking for a quick fix, and quite often conflict.
"Both in New Zealand and overseas I have been aware of high performance programmes that are successful on the medals front, but dysfunctional in a lot of other aspects, including the treatment of athletes and coaches."
Beard said they care about their people and participants.
"This includes our elite athletes. Along with a wide group of sports, we have contributed to Sport New Zealand's athlete welfare review. We look forward to outcomes from this piece of work to better understand how we can benefit our athletes' wellbeing.
"It won't end there. There will be an ongoing effort to improve. Triathlon will continue to work hard in this space and participate in any future collaborative efforts that aim to enhance the elite athlete environment."
Pilone appreciated that on the face of it New Zealand sport had enjoyed plenty of medals success at recent Olympics and world championships.
"However, I have some reservations about how the whole the high performance environment works in Olympic sports.
"Events at Triathlon New Zealand over the last six years have done nothing to cause me to revise those concerns."
