Holsted responded to him that the arrangement, which was extended to primary and area schools, was for the term of the agreement only.
"It is important that the terms of settlement are applied consistently. Fees which fall due outside the term of the agreement are the responsibility of the teacher, by agreement with the unions," Holsted wrote.
"The Secondary Teachers' collective agreement is currently being renegotiated with the PPTA and any new arrangement with respect to practising certificate fees needs to be worked through in that context. As this issue is currently under negotiation, I don't consider it appropriate to comment further at this point," she wrote.
O'Connor told the Herald it was an anomaly.
"It could be quite easily fixed and show quite considerable goodwill in the middle of collective contract round for both NZEI and PPTA.
O'Connor said his school, with a staff of 155, had processed five registrations in one day alone this week that had been declined by the ministry.
His school had paid the fees in the meantime but other schools may not be able to do that.
"It just seems petty, it's minor dollars in a big round," he said.
Act leader David Seymour said that by refusing to reimburse teachers whose registration happened to lapse while there was no agreement in force, the ministry had "decided to single out and pick on a distinct group of teachers for no good reason".
Melanie Webber, junior vice-president of the PPTA, said she had received a number of emails from upset teachers.
"Teachers see this as a real clawback in terms of their conditions and their pay. It's $220. It's a considerable amount of money for a lot of teachers, particularly in Auckland, to be paying.
"It's really unfair, when it's required as part of what you need to do your job. Other professions like doctors have them paid for them, a lot of lawyers have them paid. Why are we having to pay this to have our hideously underpaid, overworked jobs."
The PPTA had asked for the same condition to be included in any new agreement.
The NZEI said it was a condition the ministry had inserted into the previous collective agreement.
It hadn't been asked for and wasn't offered in the current negotiations.
"In putting our collective agreement claims together, our members were really focused on a significant pay jolt, time to teach, and addressing workload. That's what they're most concerned about," NZEI president Lynda Stuart said.
Seymour said the issue showed why the union model, and collective agreements were out of date for education and why teachers would be better off without them.
"This would never happen at a charter school with individual employment agreements," he said.
PPTA members are holding a series of regional ballots to decide whether to accept their latest offer, and NZEI members are holding rolling strikes this week after rejecting an offer.
