A defense lawyer for Owen Labrie claimed that a key witness in his sexual assault trial had also faced suspicions of having sex with an underage student at St. Paul’s School but avoided charges, according to recently unsealed documents in the high-profile case.

The assertions came at a private sidebar during Labrie’s trial last summer, as attorney J. W. Carney Jr. sought to undercut the testimony of Andrew Thomson, who was Labrie’s roommate.

Thomson testified that Labrie told him he had sex with the 15-year-old girl on the night of the alleged attack in May 2014. But Carney told the judge that Thomson “would have an incentive to be especially cooperative in giving the police what they wanted’’ because of complaints raised by the mother of another first-year girl, according to a transcript.

Carney also noted Thomson’s connections; his mother, Lucy Hodder, is a trustee at the Concord, N.H., private school and a former aide to Governor Maggie Hassan.

Through a spokesman, Thomson denied Tuesday that he had faced such an allegation. The lawyer now representing Labrie, however, said she would use the issue to argue Labrie did not receive a fair trial.

“I don’t think attorney Carney just came up with this on his own,’’ Jaye L. Rancourt said.

Labrie was convicted last August of misdemeanor sexual assault charges involving a minor, along with a felony count of using an Internet service to entice the teenager, who was below the age of consent. He was acquitted of felony sexual assault charges.

Labrie is appealing his conviction and has asked for a new trial based on claims that Carney did not represent him effectively. He had been free on bail but was ordered to begin serving his one-year sentence after a judge ruled that he had violated his curfew.

The discussion about Thomson took place at a bench conference during his testimony and became public last week, when the state Supreme Court unsealed a transcript.

Carney said he expected evidence to show Thomson “went out with’’ a 15-year-old student and claimed that the girl’s mother “believed that this witness had sex with the girl’’ after seeing his e-mails and Facebook posts.

Thomson was not charged, and a representative for Thomson and Hodder denied he had ever been accused of such actions. The representative added that Hodder did not intervene on her son’s behalf and would have no reason to do so because he did nothing wrong.

“Andrew did not engage in any inappropriate sexual conduct during his time at SPS and there is no allegation that he did,’’ attorney James D. Rosenberg said in a statement issued on behalf of Thomson. “These unfounded allegations appear to be part of the defendant’s trial strategy.’’

A spokeswoman for Hassan’s office said in a statement that the governor “had no knowledge of the defense attorney’s accusations’’ before news reports on the transcript emerged Tuesday. The statement noted that Hodder had left the governor’s office before Thomson testified.

Hodder took a job directing the Health Law and Policy Program at the University of New Hampshire early last year. She had served as legal counsel to Hassan since 2013.

In a statement, St. Paul’s School denied another claim Carney made at the sidebar — that Thomson had been ordered to stay away from the campus for three years while the first-year student whose mother allegedly accused him completed her studies.

“St. Paul’s School did not reach an agreement with Mr. Thomson for him to stay off campus for three years,’’ the statement said.

Neither Merrimack County prosecutors nor Concord Police could be reached for comment.

At Labrie’s trial, prosecutors argued that senior boys at St. Paul’s had sought to have sexual encounters with younger students as part of a tradition known as the “senior salute.’’

In his testimony, Thomson said Labrie told him that he had taken the virginity of the girl who accused him in the case.

“He seemed a little taken aback, but overall happy’’ after the encounter, Thomson said. “He seemed to be in a good mood.’’

Andy Rosen can be reached at andrew.rosen@globe.com. Follow him on Twitter at @andyrosen.