A police sniper who witnessed the execution of Lindt cafe manager Tori Johnson by gunman Man Haron Monis, said he was unable shoot Monis because he could not see him.

The sniper, who can only be identified by the pseudonym Sierra 3-3, struggled to compose himself as he described the shooting at the inquest into the Sydney siege.

Sierra 3-3 told the inquest he heard a gunshot from inside the cafe and saw a group of hostages running from the building about 2:03am.

The sniper said that was when he spotted Mr Johnson kneeling on the floor, but said he did not immediately think the cafe manager's life was in danger.

"I thought it was odd, I hadn't seen any [other hostages] in that position throughout the day," he said.

"I didn't form the view that there was any imminent risk or threat to him, only because I couldn't see where Monis was."

The sniper's voice cracked and he became emotional as he told the inquest Mr Johnson was on his knees for less than a minute when he saw a burst of gunfire within the cafe.

"I saw what I thought was a muzzle flash," he said.

"Then I saw [Mr] Johnson fall forward.

"I couldn't see him after that."

Sierra 3-3 told the inquest he immediately called "hostage down" twice and saw tactical police storm the cafe moments later.

Team 'did the best they could'

Counsel for the Johnson family, Gabrielle Bashir, questioned the sniper about why he did not take the chance to shoot Monis when he saw Mr Johnson kneeling.

The sniper said he could not see Monis posing an imminent threat to Tori Johnson. ( Supplied )

"At no time could I see anyone posing an imminent threat to him," the sniper responded.

"Even though Monis had a shotgun he'd just fired?" Ms Bashir asked.

"I could not see Monis," the sniper said.

When asked whether the situation could have been handled differently, the sniper conceded his vantage point had limited visibility into the cafe but he said his team did the best they could.

"We were pretty limited in what we could have done," he said.

"I think we did the best with what we could on the day."

The sniper has also told the inquest he did not have legal justification to shoot the gunman unless the hostages were in grave or imminent danger.

"I would have to be satisfied I was justified in taking a shot," he said.

"I'm no more justified in firing my firearm than a general duties officer on the street."

Counsel assisting the inquest Sophie Callan asked what the sniper would do if he was ordered to take a shot by a senior commander.

"I wouldn't respond to it, I'd have to be satisfied myself," the sniper replied.

Missed shot would put hostages in greater danger: sniper

Sierra 3-3 told the inquest he would have to be "100 per cent" certain any shot he fired would kill or incapacitate the gunman to the point of "flaccid paralysis".

He told the inquest the consequences of firing a shot he was not fully confident of could be "catastrophic" and could have put the hostages in greater danger.

Asked whether he and the two snipers he was stationed with believed they had a viable shot, Sierra 3-3 replied: "It wasn't great."

"The discussion was it was not an ideal situation," he said.

"Having two mediums of glass to [fire] through, the potential hazard that would cause if the shot missed, the risk to those inside - all of these things greatly reduced our confidence.

"However if there is an imminent or life-threatening situation occurring, we would attempt to act, as acting is better than doing nothing."

The sniper said he did not have legal justification to shoot the gunman unless the hostages were in grave or imminent danger. ( Getty Images: Joosep Martinson )

The inquest heard Sierra 3-3 glimpsed Monis inside the cafe several times throughout the day and about 5:00pm he could see the gunman stationary in one of the cafe's windows.

But Sierra 3-3 told the inquest he did not take a shot because he could not be certain the person was Monis, or whether any hostages were in the line of fire.

"At the end of the day it was an option," he said.

"Both for justification reasons and not knowing what was behind [Monis].

"I was quietly confident it was him but I wasn't 100 per cent certain."

Earlier this week the inquest heard that police radios failed as the critical call was made to storm the cafe after Monis executed hostage Tori Johnson.

The inquiry continues.