The allegations were outlined in a recent report by Vice News.
Tim Ballard, the former Homeland Security operative whose life served as the basis for the film, stepped down as CEO of the nonprofit Operation Underground Railroad in June.
Reporters at Vice cited unnamed sources who have familiarity with an internal investigation into the women claiming Mr Ballard engaged in sexual misconduct.
Operation Underground Railroad confirmed to Vice that it had hired an outside law firm to investigate, but did not provide further details.
Though Mr Ballard has not provided a response to Vice for its report, he has previously insisted that Vice's other reporting about him was "not true."
In a statement after publication, Mr Ballard called the allegations “baseless”.
“As with all of the assaults on my character and integrity over many years, the latest tabloid-driven sexual allegations are false. They are baseless inventions designed to destroy me and the movement we have built to end the trafficking and exploitation of vulnerable children. During my time at O.U.R., I designed strict guidelines for myself and our operators in the field. Sexual contact was prohibited, and I led by example. Given our meticulous attention to this issue, any suggestion of inappropriate sexual contact is categorically false.”
Mr Ballard became a subject of scrutiny after the release of the film "Sound of Freedom," which was beloved by conservative movie-goers, with some right-leaning groups buying out entire theatres to provide free screenings to others.
Operation Underground Railroad admits on its site that some parts of the movie are fabricated and do not parallel the truth of Mr Ballard's life. It also acknowledges that the kind of child trafficking portrayed in the film is the exception, not the norm. Organisations that fight child sex trafficking criticised the film for its portrayal of the sex trafficking industry, noting that the majority of trafficking incidents involve families selling other family members, as opposed to the abductions portrayed in the movie.
The QAnon conspiracy movement long held that elites – especially Democrats and other ideological enemies – sex trafficked and even devoured children.
The allegations against Mr Ballard claim he pressured women working at the organisation to act as his "wife," coercing them to share his bed and shower with him during supposed anti-trafficking missions.
He allegedly told them it was a way to trick traffickers and helped him in his mission to save minors, according to the report.
One of the sources said Mr Ballard sent a photo of himself in underwear to at least one woman, and asked another "how far she was willing to go" to save trafficked children.
Vice reportedly attempted to contact the women and get them to speak on the record, but suggested they were unwilling to go public for fear of retaliation.
Operation Underground Railroad said in a statement that it does not tolerate any sexual harassment or discrimination in its orgnisation.
"O.U.R. is dedicated to combating sexual abuse, and does not tolerate sexual harassment or discrimination by anyone in its organisation," the group said in a statement to Vice.
The group said that the outside law firm was investigating "all relevant allegations" but would not offer further comment.
A previous report by Vice and local media in Utah claimed that Mr Ballard was condemned by the LDS Church, which Mr Ballard denied during an event.
"It's not true, nothing you hear is true," Mr Ballard said, referring to a local media piece about his condemnation.
The Independent has reached out to Mr Ballard for comment.