Jones's death led to nationwide calls for a push for improved safety standards on sets.
His allegations were reported on the BBC Spotlight programme last night.
Mr McGahon and another man allege the offences took place at an identified location in County Louth.
Greg Allman biopic train death trial ends
Greg Allman biopic train death trial ends
The 27-year-old was fatally struck after the crew placed a hospital bed on the railway tracks in Doctortown while filming a dream sequence.
Complaints were made to police in Drogheda towards the end of last year.
Earlier, Mr Adams said he only found out about the incident in 2009 when he was told by Sinn Féin Louth TD Arthur Morgan.
Irish police have confirmed that a file is being prepared for the Director of Public Prosecutions over the alleged sexual assault of two males in County Louth in the 1990s.
Assistant district attorney John B Johnson said Sarah Jones' family was "satisfied with the outcome".
Investigators found CSX Transportation, which owns the railroad bridge, had denied the film-makers permission to work on its tracks.
Paudie McGahon has told BBC Spotlight he was raped as a teenager by an alleged IRA man and that the IRA later subjected him to a "kangaroo court"
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瀏覽原文:/news/entertainment-arts-31832656
Miller was sentenced to two years in the Wayne County jail and an additional eight years on probation.
The trial over a fatal train crash on the set of a biopic about the singer Gregg Allman has come to a close.
Assistant director Hillary Schwartz was the final person to be convicted over the accident, which killed camera assistant Sarah Jones.
On Wednesday, Ch Supt Pat McGee confirmed that "the investigation is ongoing and a file will be sent to the DPP in due course".
He said he was later subjected to an IRA "kangaroo court" after a Sinn Féin representative was told of the allegations.
Allman sued Miller in civil court last year to prevent the director from reviving the project. They settled out of court but terms were not disclosed.
來源：Bbc 更新時間：2016-03-12 10:29:35 分類：News
Her father Richard Jones said he hoped "the sacrifice of our daughter's life will continue to change the film industry".'
Jones was hit by a freight train on 20 February 2014 - the first day of filming on Midnight Rider - in south east Georgia.
Sedrish received 10 years' probation which bars him from directing or serving as a first or second assistant director or crew supervisor, plus a $10,000 (?6,700) fine.
He said Mr McGahon's alleged attacker should come forward.
Ms Schwartz waived her right for trial by jury and opted for a judge to decide her case.
His guilty plea included a deal which saw charges dropped against his producer wife, Jody Savin.
In the BBC programme, Mr McGahon said the IRA offered to kill the alleged rapist but instead expelled him to England.
William Hurt had been cast as Allman (pictured) in the film
Speaking to reporters outside the court on Monday he said: "I believe it sends a message, frankly, that if you do not respect those you're in charge of, you may end up behind bars.''
The director of the film Randall Miller and executive producer Jay Sedrish pleaded guilty on Monday.
The director, whose previous films include 2008's Bottle Shock, will also pay a $20,000 (?13,200) fine and work 360 hours of community service.
When asked on Wednesday by Irish broadcaster RT? about Mr McGahon's claims that he was subjected to internal IRA inquiries, Mr Adams said: "I don't know - the fact is there is a Garda [police] investigation under way."
Filming was suspended in the aftermath of the accident, and actor William Hurt - who was due to play Allman - pulled out of the production.
Earlier, Sinn Féin leader Gerry Adams said he believed Mr McGahon's story about being raped, however, he did not clarify whether he believed his claims that he was subjected to an IRA "kangaroo court".
The train, which was travelling at 55 mph, shattered the bed, sending a shower of debris that injured other crew members.
Jones, who had been setting up camera equipment, died instantly when she was struck by the train's fuel tank and run over.
11 March 2016Last updated at 16:56
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Greg Allman biopic train death trial ends
Miller, pictured during an earlier court appearance, will spend two years in county jail
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He told the BBC's Spotlight programme that an IRA man, from a well-known republican family in Belfast, abused him and then threatened him to remain silent.
Six other crew members were also injured when they were hit by a train in February last year.
瀏覽原文:/news/uk-northern-ireland-31844625
Mr McGahon said he wanted the republican movement to acknowledge the truth of his story.
One of the complainants is Paudie McGahon, 40, who has alleged that he was raped by an IRA man when he was 17.
She was sentenced to 10 years' probation and a $5,000 (?3,300) fine.
They admitted involuntary manslaughter and criminal trespassing to avoid trial.
Paudie McGahon has told BBC Spotlight he was raped as a teenager by an alleged IRA man and that the IRA later subjected him to a "kangaroo court"
