Yipirinya, the largest Indigenous school in Central Australia, has responded after Principal Gavin Morris was charged with multiple counts of aggravated assault against children.

Dr Morris was charged by NT Police with five counts of aggravated assault on Thursday and is due to face Alice Springs Local Court on August 13.

Yipirinya has 380 students, all of whom English is not their first language, with the majority of the school's staff Indigenous.

In a statement, the school said it was "deeply concerned" about the allegations.

"We want to assure our community that the safety, well-being and education of our students is our highest priority," the statement said.

"While the investigation continues, Yipirinya School remains committed to transparency and cooperation with the authorities. The Yipirinya School believes in due process and will fully cooperate with any ongoing investigations."

In a statement on Thursday after Dr Morris' arrest but before he was officially charged, NT Police said: "On 20 June 2024, police received reports of historic physical assaults on children at the school. It is believed the alleged assaults occurred on multiple separate occasions in 2023."

"The six victims were aged between eight and 13 years old at the time of the assaults, and police will allege the man was an employee of the school at the time," NT Police said.

Yipirinya said the school will remain fully operational, with staff focused on "providing a secure, safe and nurturing environment for every child".

"We urge parents and the school community to reach out with any concerns or questions they may have," Yipirinya said.

"Our top priority is to uphold the trust of our local community, while continuing to provide an enriching education for our kids during this time.

"As a community, this is a time of shock and sadness, and we respectfully request privacy around our school grounds to protect the students and staff as they navigate this difficult situation."

Dr Morris' status as principal remains unclear, with Yipirinya saying they wouldn't be making further comment at this time.

Also on the Alice Springs town council, Dr Morris has been an advocate for Indigenous children in the Red Centre, as well as for the town in general.

He has previously spoken about the "crisis" impacting Alice Springs' youth, previously highlighting how staff have needed to contact magistrates to have bail conditions altered for children in order for them to participate in after-school programs.

The school has been promoted by Opposition Indigenous spokesperson, Senator Jacinta Nampijinpa Price, whose mother, Bess Price, is on the school faculty.

Ms Price has previously argued for more funding for Yipirinya and the need for a specialist boarding facility.