More than 5000 teachers working in schools across the country in the last year were unauthorised, while another 400 did not appear on any Teachers Council records, the organisation's annual report says.
By matching its own records against the Ministry of Education's payroll information, the Teachers Council discovered the discrepancy.
It found 5045 teachers working in schools whose authorisation to teach had expired, and a further 433 teachers who were being paid but were not listed on the council's data for the 2013-2014 year.
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Rob McIntosh, acting director of the Teachers Council, said the vast majority of the cases identified were simply an administering issue.
"Most of [the 5045 cases] are people who have been registered and whose practising certificate has lapsed, either because of oversight or because they are assessing their situation," he told Radio New Zealand this morning.
"So what we do is we follow up with them, we write to them, we write to the principal, and many of those instances the situation is rectified.
"For another group of people, there is the capacity to teach in New Zealand schools for up to 20 half days without registration. That's most often what we find in the other group of people we identify. Those people, again, are teaching within the law, and because they're doing it without registration they're not known to us, but through this process they become known to us."
The fact the council uncovered these cases proved it was a "robust" system, in place to ensure safety in schools.
"This is why we run this process, to ensure that no teacher slips through the cracks and shouldn't be teaching at all in our schools," he said.
"We use this information to identify the people, we follow up with them, and we ensure that either they become registered, as they should be, or they stop teaching if they have no authority to teach."
Asked what kind of assurance he could give to parents worried about a repeat of the Te Rito Henry Miki debacle, in which the convicted sex offender taught in six schools under a new name, Mr McIntosh said: "The assurance is that we're actually doing this process, that we're transparent about it and we are actually checking. We're exchanging data with the ministry and following up, writing to schools and principals, and making sure that every case we identify is dealt with and the situation is put right.
"It's actually a very robust part of our processes."
Also mentioned in the annual report was a "continuing upward trend" in the number of conduct and competence cases being brought before the council's disciplinary board.
The council received 90 reports or complaints about teacher competence, up from 58 the previous year, and resolved 436 conduct and conviction cases, more than the 345 dealt with in the 2012-2013 year. On top of those, 55 cases were referred to the disciplinary tribunal, up from the previous year's 39.
"The council believes that this is due to the profession becoming more confident in and more aware of the importance of the council's disciplinary processes, rather than there being an underlying increase in conduct and competence issues," the report said.