A man accused of trespassing on Pine Gap, the joint defence facility outside of Alice Springs, was there to sing and pray for the Arrernte people, the Alice Springs Supreme Court has heard.

Cairns man Paul Christie, 44, is on trial this week accused of entering a prohibited property under the Defence Special Undertakings Act.

Lloyd Adams, who is a Protective Service Officer with the Australian Federal Police (AFP), told the jury Christie was carrying a satchel at the time of his arrest which contained a pocket knife, small stick and a map.

"He had no permission to be in that area," he said.

The court heard a person in a red-hooded jacket was first spotted inside the facility on CCTV at 6:30am on October 3, 2016.

The facility, outside of Alice Springs is off limits to the public. ( Supplied: Kristian Laemmle-Ruff )

Crown prosecutor Michael McHugh SC told the jury Christie was arrested inside the facility, about 1.5 kilometres from its northern boundary fence.

"The accused was found inside a prohibited area … and he was reckless to whether or not it was a prohibited area," he told the court.

Prosecutor McHugh said Christie entered via a dry creek bed and told police officers at the time Pine Gap was on stolen land and he was there to sing and pray for Arrernte children, the traditional owners of Alice Springs.

He did not hold a permit to be on the prohibited site but the court heard he did not resist arrest when AFP officers spoke to him, and voluntarily dropped to his knees and put his hands behind his head.

Protestors were outside the Supreme Court chanting messages against the Pine Gap facility. ( ABC News: Claire Campbell )

An AFP officer who works at the Pine Gap facility, Matthew Gadsby, told the court Pine Gap was surrounded by a barbed wire fence up to three metres in height, with "no trespass signs" located every 40 metres.

Christie, who is self-representing himself in court, questioned Mr Gadsby on whether someone being on the site posed a threat to the facility.

"Yes, he did … he's in a prohibited area," Mr Gadsby responded.

Outside the Supreme Court, a small group of protestors had set up banners reading "Close Pine Gap" and were singing and chanting as court proceedings got underway.

The trial continues.