The Northern Territory Education Department was trying to fix an embarrassing blunder on Friday after nearly 600 teachers had to be pulled from classrooms because they did not have working with children clearances.

The teachers were barred on Thursday, affecting the majority of the Territory's schools, and many were still unauthorised to work with kids by Friday.

Principals had to frantically organise alternative classes for students and find other duties for some teachers or send them home.

The department admitted it only knew of the backlog of clearances, known as Ochre Cards, when the Australian Education Union told them after teachers raised worries.

Nurses, doctors and other professions were also affected with some unable to work because of the backlog at the NT Police-operated Safe NT.

NT branch secretary Adam Lampe described it as a terrible "screw up" that children were paying for.

Education Department CEO Vicki Baylis defended the bungle, saying it was a "perfect storm of volume" due to a large number of new teachers in the NT and others due for renewal.

She said parents that were worried should know their children were safe and teachers had to meet a high ethical threshold that also included being on the government Teacher Registration Board.

Some 458 teachers had been processed by Friday but there were more than 130 still to be cleared with people subject to the National Police Check service.

Deputy Opposition Leader Lia Finocchiaro said it was a debacle that was stopping key frontline services such as education and health that people rely on being delivered.

"This breakdown in leadership is really unacceptable, something like this needed to be sorted a long time before it became a problem where 600 teachers couldn't be in front of students," she told reporters.