An elite Australian soldier has told a judge he was "perplexed" after witnessing an Afghan man's execution in 2012, saying it was at the direction of decorated war veteran Ben Roberts-Smith.

Mr Roberts-Smith is suing The Sydney Morning Herald, The Age and The Canberra Times newspapers over a series of stories that included allegations of unlawful killings overseas, which he denies.

An active SAS member, given the pseudonym Person 14 and called by publisher Nine Entertainment, today told the court about a mission in Khaz Oruzgan in October 2012.

Person 14 said he heard a radio call to prepare for extraction, signalling helicopters were about half an hour away.

He told the court he was present in a room where Mr Roberts-Smith was with a group that included Person 12, a member of the Afghan Partner Force, and an interpreter, Person 13.

Also in the room was a local Afghan man, who the witness described as "slender, middle aged" and wearing traditional robes.

Person 14 said a colleague told him "they're just questioning this bloke", before he kicked a "discoloured" area of the building's wall and discovered a hidden weapons cache.

The court heard items including bags of bullets, binoculars and rifles fell from the cache, which engineers began to inspect.

"The mood had changed," Person 14 said.

The witness claimed Mr Roberts-Smith told the interpreter: "Tell him to shoot him or I will."

The court heard there was a discussion between the interpreter and Person 12 in an Afghan dialect before one of their soldiers, who was wearing a balaclava, stepped forward from a group.

"(He) trained his suppressed M4 on the Afghan man and unloaded five to eight rounds into the … torso, the chest," Person 14 said.

"He (the Afghan man) dropped, and then at least another two rounds up around his head area, neck area.

"I was perplexed but didn't say anything."

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The witness said another colleague, Person 26, was the troop sergeant and appeared to be unhappy.

"He said 'what happened to the f ****** PUC (person under confinement)'."

Person 14 earlier told the court details of a separate mission in 2009, when Australian patrols were clearing a Taliban compound dubbed "Whiskey 108".

He recalled how his colleagues were discussing "re-manoeuvring" their location to provide greater coverage outside the compound when he heard heavy footsteps and "chatter".

He said he then saw three Australian soldiers and "a black object which was similar to a human" being thrown to the ground with a "thud".

"There was kind of a noise, (an) expulsion of air when someone is winded, and then a soldier raised their Minimi F89 Para and fired like an extended burst," the witness said.

He imitated the sound of the weapon in the witness box.

"It was loud … one second. That person turned and walked away out of sight towards Whiskey 108."

Person 14 said he couldn't identify the soldier who fired, however the weapon they had was "distinctive" and not carried by many people.

The court heard he later saw Mr Roberts-Smith was carrying the same weapon at their "lie up position".

Earlier this week, another SAS witness claimed to have seen Mr Roberts-Smith "frogmarch" an older Afghan man out of the compound, throw him on the ground, and shoot him in the back with "three to five rounds".

Mr Roberts-Smith has previously denied wrongdoing during his own evidence and insisted an enemy he shot that day was armed and rounding a corner of the compound.

Person 14 told the court he turned to his second-in-command and said: "What the hell was that?"

"How did he respond?" barrister Nicholas Owens SC, for Nine, asked.

"Non-verbally, he shrugged his shoulders … alluding to, he doesn't know," Person 14 replied.

The witness said he later inspected the "black object" and confirmed it was a dead Afghan male with blood "generally concentrated around the upper torso".

"He was laying on his back, he had a shaved head, a little bit of a beard, dark Afghan robes, he had like … a white leg, which ended up being a prosthetic leg," he said.

Person 14 said there was no weapon near the body.

He also told the court he later saw the dead man's prosthetic leg "wedged" in the plate carrier, or armoured vest, of one of his colleagues, Person 6. 

"He had created like a zigzag bungee cord, elastic you could shove items in other than put them in your actual pouches," he said.

"In there, wedged in, was the leg."

Person 14 also recalled later seeing the leg in the Fat Ladies Arms, an unauthorised bar, where it was used as a drinking vessel, including by him.

He said he wasn't aware of Mr Roberts-Smith ever drinking from the leg, which he also saw in the unit barracks in Australia.

The trial, before Justice Anthony Besanko, continues.