A security official, speaking on condition of anonymity in line with regulations, said the fatal bullet would likely be a key piece of evidence in the investigation.
United Nations’ investigators are trying to establish whether the death of the Irish peacekeeper was an ‘opportunistic’ killing or part of a planned attack.
Private Rooney died as he desperately tried to steer himself and three colleagues to safety after coming under fire in Lebanon.
The nature of his death is being viewed as murder in Irish military circles.
The circumstances which led the Irish unit off an approved route from their base to Beirut Airport will be central to the investigation.
Eight members of the Defence Forces were travelling in two armoured SUVs when they somehow became separated.
Pte Rooney’s vehicle was then surrounded by a mob in the village of Al-Aqbiyah which is under the control of the militant group Hezbollah.
The organisation has denied involvement in his death but Defence Forces Minister Simon Coveney has not accepted their version of events.
Trooper Shane Kearney (22) was also seriously injured when two other officers sustained less serious wounds.
It is expected that Pte Rooney’s family will be offered a funeral with full military honours for the 23-year-old, but it is up to them to decide if they want such a public event.
It is understood that the Government jet will be deployed if this is deemed necessary to speed up the process.
The group of soldiers were travelled to the airport to drop off two men who had been given compassionate leave to travel home for separate funerals.
They set out on two and a half hour journey which would be considered routine for officers in the area.
How the two vehicles became separated will be a major part of the investigation. It was after dark, but the route chosen by the convoy was a “well-trodden” one.
As yet, there is no explanation for how the vehicle ended up on an unauthorised road. But army personnel who have served in Lebanon say it is easy to take a wrong turn at that time of night.
It’s understood that neither vehicle had satellite navigation tools onboard owing to sparse signal along much of the route. A number of lines of inquiry are expected to be developed in the coming days.
Sources said they don’t know if the attack was “opportunistic” because the soldiers accidentally ended up in the area or whether “something more planned” occurred.
Investigators have reviewed several videos of the incident, which were circulated locally in the aftermath of the attack.
In one, which was shot from a third-floor apartment balcony, the Irish unit can be seen driving at speed while what appears to be bullets are hitting the vehicle.
One line of inquiry is that their vehicle overturned after it hit a pylon while trying to flee the gunfire.
However, investigators have not ruled out the possibility that the jeep was physically overturned by a mob.
The jeep is understood to have been less than a year old. Photographs clearly show damage caused by a series of bullets hitting the windows and door panels.
The glass on armoured vehicles is designed not to break even if hit with bullets.
One theory being probed by the Defence Forces is that the doors of the vehicle carrying Pte Rooney were unlocked due to the impact of the crash. This allowed the aggressors access through the boot.
It is not clear whether Pte Rooney died as a result of a bullet penetrating through the vehicle – but one theory under investigation is that he was killed outside of the vehicle after it overturned.
His colleagues are standing guard over his body at a UN hospital and will remain there until repatriation takes place.
A time for him to be flown home has not yet been established, but it will be in a matter of days.
Trooper Kearney also suffered a non-life-threatening bullet wound but is believed to have suffered significant head injuries on impact. He underwent major surgery and remains in critical condition in a UN hospital.
One source said that either way it could be considered a murder as the men were not engaged in combat. Two members of the unit who crawled from the vehicle were not shot.
Local media reports said that residents of the southern town of al-Aqbiyah, just outside Unifil’s area of operations in south Lebanon, have confronted the Unifil convoy for taking a different route than the agreed and usual one they travel to Beirut.
It has been reported that youths in the area followed the convoy and blocked its way.
Pte Rooney was a native of Newtowncunningham in Donegal, was described last night as a “model soldier” who was known for his kindness, dedication and sense of humour.
Speaking to Independent.ie, a colleague of Pte Rooney’s and Trooper Kearney said: “It could have been anyone killed like that.
“It is easy to take a wrong turn, particularly at night. It is pitch black. Night is the worst time to travel to Beirut.
“It happens sometimes two or three times on every tour, a convoy goes down the wrong road and is surrounded.
“Usually, they just frighten you. If you have an interpreter with you, they can go and explain, but this obviously didn’t happen.
“There are two routes. The long one and the short one.
“The one by the sea, if you did it once, you would know it. But the one through the mountains, which is way shorter, is hard to even follow during the day. Unless you know the way it is so easy to take a wrong turn. There are no road signs and no lights.
“It is only in recent years that Irish soldiers were allowed to drive over the mountains, which takes approximately two hours while the other is 3.5 hours.
“Over the mountains, particularly at night, it’s very easy to get lost.
“There are about 10 turns in it. The golden rule is that the UN is not allowed on many roads because Hezbollah doesn’t want you to see what they are doing.
“This was definitely an accident because you don’t go down roads you don’t know in the Leb, especially at night.”
The Irish Defence Forces are to deploy a special team to Lebanon in a bid to find out what led to the death of Pte Rooney.
A team of eight officers, including specialists in stress management, will also assist soldiers still on the ground in dealing with the tragic loss of their colleague.
Minister Coveney has said Ireland “will demand the truth’ following the tragedy.
There will be three investigations into the killing, including one by the Irish Defence Forces. Three military police officers and a legal advisor will travel from Ireland.
The UN will carry out its own independent probe, and the Lebanese Army will do likewise.