Northern Territory police commandeered a Royal Flying Doctor Service (RFDS) plane to deceive a remote Indigenous community after an officer shot dead a young Aboriginal man during a botched arrest, an inquest has been told.

Kumanjayi Walker, 19, died after Constable Zachary Rolfe shot him three times in Yuendumu, northwest of Alice Springs on November 9, 2019.

In the hours after, police concocted a ruse to make community members believe the Warlpiri man was still alive amid fears officers could be killed.

“It was deliberate in its deceit and about giving the perception (Mr Walker) was being conveyed (to hospital),” Superintendent Jody Nobbs told the coroner on Tuesday.

“The police plane that came in was a leased RFDS plane so it was badged as an RFDS plane, which further supported that.”

But the plane wasn’t deployed to collect Mr Walker, who had died on the local police station floor. It was instead used to evacuate Constable Rolfe and carry members of the police tactical response group into the community.

Officers in Yuendumu drove in a convoy with an ambulance to the plane from the police station compound, where up to 200 community members had gathered out of concern for Mr Walker.

Superintendent Nobbs, who coordinated the police response to the shooting from Alice Springs, said the ambulance was a useful prop to reinforce the ruse and it later also helped carry the reinforcements’ equipment back to the station.

“I did have an appreciation of the cultural deceit that was inherent in the plan but elevated … the broad community safety over the cultural sensitivities,” he told the inquest, now in its fourth week.

“It has deeply troubled me and I acknowledge it has deeply troubled the community ever since.”

Superintendent Nobbs also made the decision not to let Mr Walker’s family comfort him as he died.

He said he was aware of his cultural insensitivity but had to consider the safety of the seven officers inside the police station, including the man who pulled the trigger, Constable Rolfe.

“There was a large swelling of the crowd that was varying degrees of hostility and aggression out the front of the police station,” Superintendent Nobbs said as he recounted the night, including a cancelled plan to evacuate all police from the community.

Earlier, Superintendent Nobbs told the Alice Springs court he sent Constable Rolfe and his team to Yuendumu but he hadn’t authorised the men to undertake the early evening arrest they did.

He said the plan was to wait until early the next morning after a culturally significant funeral when the officers could take Mr Walker into custody without the use of force.

But Constable Rolfe and his team didn’t wait and instead searched house to house armed with an AR15 assault rifle and a shotgun under the guise of “intelligence gathering” until they found Mr Walker.

Asked if the team should have been armed with the high-powered weapons, Superintendent Nobbs said: “No”.

“The night activities were (supposed to be) about reassurance … to the broader community so I found it counter-productive,” he said.

“There was no elements around an intelligence gathering exercise so that was outside the scope of my clear instruction.”

Asked if the team’s actions were those of a “disciplined force that’s following a plan”, Superintendent Nobbs said: “No”.

The heavy impact the shooting has had on the NT police force became evident when counsel assisting Peggy Dwyer showed Superintendent Nobbs body-worn camera footage recorded by Constable Rolfe’s team before Mr Walker was killed.

Superintendent Nobbs struggled to watch it, saying: “It’s a difficult one for me … This event has had a deep impact on everyone involved, but it certainly has on me as well”.

“I spent probably six months not sleeping, going how can something so simple in my mind have become what it ultimately became.”

The hearing continues on Wednesday.

Get local, national and world news, plus sport, entertainment, lifestyle, competitions and more delivered straight to your inbox with the Canberra Daily Daily Newsletter. Sign up here.