Harris said she could make no comment on any incident until reviews of the World Equestrian Games and annual High Performance Sport New Zealand funding were complete.
HPSNZ chief executive Alex Baumann could not be contacted for comment on whether it would affect equestrian's annual funding, or if mediation was under way.
ESNZ received $2.05 million of taxpayer high performance funding this year and are scheduled to receive $7.45 million across the 2013-16 cycle. However, that investment is weighted towards the presence of the 53-year-old Nicholson, who picked up his fifth Burghley title, and third in a row on Avebury, this year.
Nicholson doesn't believe optimum care was provided for his horse during the World Equestrian Games. He alleges Nereo was left without veterinary assistance on several occasions and that he had to find someone to phone the vet and track them down.
"That's not what you expect at a world championships for a horse of that calibre," he said. "Also, there were only two horses - [the other being Jonelle Price's Classic Moet] - to look after at that stage of the competition.
"That was the sole basis for why I was angry. I regret the incident but I'm not going to apologise.
"There was a robust discussion and an argument. Two members of the management team, Sarah Harris and Erik Duvander, signed the complaint against me.
"We had subsequent discussions where I said, 'I can't believe how you're treating me. I'm removing myself from the [2015] high performance squad'. They subsequently withdrew their complaint and I wasn't asked to apologise."
Nicholson will compete as normal next year and his self-imposed exile will make little material difference given there are no team competitions scheduled in the next 12 months.
He's likely to compete at an eighth Olympic Games in Rio in 2016, when a strong New Zealand team is likely to be assembled. He's previously won three team medals but is still chasing an elusive individual medal - he finished fourth in London.
Nicholson will not contemplate relaxing his stance regarding the high performance squad until the debriefing of the event is complete and his concerns have been listened to in full.
"I'm placing faith in the high-performance review process to help rectify the problems. Ultimately, the team didn't deliver at the World Games, despite significant government funding. We have to be realistic in reviewing that."
Price's fourth place was the best finish by a New Zealander at the World Equestrian Games. Nicholson was ninth.
The other team riders - Sir Mark Todd, Jock Paget and Tim Price - did not finish.
The incident continues a difficult period for ESNZ in the wake of Jock Paget's year-long ban after his horse, Clifton Promise, tested positive for a prohibited substance at last year's Burghley. He was cleared this year and returned to competition.
