The Fair Work Commission has ordered the Australian Education Union's Northern Territory branch to suspend its protected industrial action for three months, amid claims from the NT Government that the union was encouraging teachers to "ignore their duty of care" to students.

The order from the Commission, which is effective from today, came after the union instructed teachers not to enter attendance data into the electronic Student Administration Management System (SAMS) database and to only perform their duties during "normal" working hours (7 hours 21 minutes each school day).

The NT Minister for Public Employment John Elferink claimed the union's directive was dangerous given there would be no way to assess if a child was present at a school in the case of an accident or emergency.

“When parents send their children to school, they expect that the regular, necessary processes will be followed to ensure their child’s safety, yet this has been disregarded,'' he said in a statement.

"“The Union’s tactics over the Enterprise Bargaining Agreement (EBA) negotiations directly affect children’s safety. Parents expect better care of their children. This crosses the line,'' he said.