A Sydney siege sniper has described seeing cafe manager Tori Johnson on his knees before being executed, and how hours earlier he had the hostage-taker in his sights but did not think he had authority to shoot.

The senior constable, who is the first sniper to give evidence at the inquest into the December 2014 siege of the Lindt Cafe, became emotional as he recalled seeing a muzzle flash and Mr Johnson then falling forward.

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Identified only by the call-sign “Sierra 3-3”, the Tactical Operations Unit member was part of a team of marksmen who had taken up positions at the Westpac building diagonally opposite the cafe.

He said it was a matter of 30 seconds to a minute between the moment he observed Mr Johnson on his knees and the muzzle flash, believed to be the moment gunman Man Haron Monis executed the cafe manager at about 2.13am on December 16, 2014.

Man Haron Monis was on bail at the time of the Lindt Cafe attack. Photo: AAP.

“I was trying to look for Monis at the time as there’d been a shot fired,” he said, referring to the escape of six hostages 10 minutes earlier, which had prompted the gunman to fire off a round from his shotgun for the first time.

“My focus was drawn on what I thought was Tori,” he told the inquest on Wednesday. “It appeared to me he’d taken a lower profile because I could only see him from the waist up which made me think he was on his knees.

“I saw what I thought was a muzzle flash then I saw Mr Johnson fall forward. I couldn’t see him after that.”

Police stormed the building after Mr Johnson was killed, bringing an end to the siege. At various times during the more than 17 hours of the stand-off, snipers at Westpac as well as the Channel Seven building directly opposite the cafe and the Reserve Bank observed Monis through windows but could never be “100 per cent” about having a good shot.

Sierra 3-3 also doubted whether he had legal authority.

“Having two mediums of glass to get through, the potential hazards that would cause if the shot was missed, the risk to those inside; all of those things greatly reduced our confidence,” he said.

Asked about the legal justification for taking a shot, he said: “I’m no more justified in firing my firearm than a general duties officer on the street”.

Police stormed the cafe after Mr Johnson’s death initiated the police Emergency Action plan, the triggers for which were death or serious injury or imminent death or serious injury.

Asked by counsel assisting the Johnson family, Gabrielle Bashir SC, why Johnson being ordered to his knees by a man who had sworn allegiance to Islamic State did not represent an imminent threat, Sierra 3-3 said he could not see Monis at that time.

“At no time could I see anyone posing an imminent threat to (Mr Johnson).”

Monis was killed by police, while hostage Katrina Dawson died after being hit by fragments from police rounds.

The inquest continues.