Changes have been made to after-school transport procedures after a primary school student mistakenly boarded a bus to a Darwin immigration detention centre earlier this week.

The Northern Territory Education Department says the girl, who was starting grade two at Anula primary school, boarded a bus for asylum seeker children after school on Monday.

Usually, before getting on the bus, asylum seeker children who attend classes at the school are counted and ID tags are handed to Serco officers.

In this case, however, the child, who is of Indonesian background, managed to board the bus without handing over ID.

It is believed she followed a friend on to the bus.

The mistake was discovered while the girl was en-route to the Wickham Point immigration detention centre.

School officials then drove to pick up the girl and returned her to the school, where her father was waiting.

Anula primary is one of the Darwin schools that cater for children in detention.

The Education Department says the Anula school principal has met with Serco representatives since the incident and new procedures have been put in place.

Serco, a private company contracted to run detention centres in Australia, has declined to comment on what those new procedures are.

The Immigration Department says the child did not enter the detention centre.