Coroner Jim Kitson is to assess whether the case on the death of 11-year-old Francis Rowntree in Belfast in 1972 should be handed over to the region's Director of Public Prosecutions Barra McGrory.
Under legislation, a coroner is obliged to refer a case to the DPP if evidence of a potential criminal offence emerges during an inquest process.
A new inquest into the killing was ordered by Northern Ireland's Attorney General John Larkin in 2012.
At a preliminary hearing in Belfast on Wednesday morning, Mr Kitson made the unexpected disclosure.
"It is something I have to consider and there's no latitude in that," he told lawyers.
The coroner has previously been told that the soldier who fired the rubber bullet, known only as soldier B, would not be able to give evidence at the inquest due to ill health.
On Wednesday, lawyers for Francis's family urged Mr Kitson to order an independent medical assessment to test this claim.
It has also emerged that a teenage witness to the shooting, who had been sought through a media appeal, has now come forward.
Francis was hit by the rubber bullet fired by the Royal Anglian Regiment soldier as he played with friends at the Divis Flats complex close to the Falls Road in April 1972.
He died four days later from injuries including a fractured skull.
Controversy surrounds the shooting, with disputed claims on whether the young boy was struck directly or hit by a ricochet, and if the bullet had been doctored to make it potentially cause more injury.
There have been previous inquest cases referred to the DPP, but usually after the proceedings have concluded.
The fresh inquest into the schoolboy's death is still in its preliminary stages and has yet to start formally hearing evidence.
However, papers related to the shooting have been assessed by Mr Kitson.
The coroner asked for formal submissions from legal representatives in the case on the issue of referral but on Wednesday asked for their initial reaction.
He insisted he had not reached a final decision on the issue.
"I have an entirely open mind on the matter," he said.
Francis's brother Jim Rowntree was in court as his barrister Fiona Doherty expressed reservations at the timing of a potential referral.
"I can say, having consulted in a preliminary way with my client, that we would have concerns about such a referral," she said.
The lawyer added: "This inquest and its potential effectiveness could be essentially stymied by any referral to the director because of the length of time it could take."
The lawyer claimed that one case referred to the DPP in 2011 was still awaiting a direction from prosecutors.
She said that, as the shooting happened so long ago, time was of the essence in regard to hearing evidence from inquest witnesses.
After the hearing, Mr Rowntree said he wanted the inquest into his brother's death to conclude before any direction was made to the DPP.
"The family would not like it to be going to the DPP because we see the delays that there is now and, no matter what, there is always some other barrier put in front of it," he said.
Mr Rowntree said his 89-year-old mother Theresa was keen for the inquest to proceed.
Ken Boyd, representing the Ministry of Defence, also raised concern in regard to the potential impact a referral would have on the inquest's time frame.
He said the MoD may need some time to consider its formal submission on the issue, potentially a number of months.
Mr Kitson replied: "I would have thought this would be capable of being dealt with in a much tighter time frame than months."
The coroner provisionally gave the lawyers four weeks to formulate submissions.
The Rowntree family's lawyers had been searching for a witness, aged 14 at the time, who in the wake of the shooting gave an anonymous account to an anti-plastic bullet campaign group.
After the hearing, family solicitor Padraig Ó Muirigh confirmed the witness had now come forward and provided a new statement for the inquest.