The incident described occurred on Snyder's private plane.
The Washington Football Team paid a former female employee $1.6 million as part of a confidential settlement in 2009 after she described sexual misconduct by owner Dan Snyder, according to The Washington Post.
The incident the employee described occurred on Snyder's private plane on a flight returning from the Academy of Country Music Awards in Las Vegas, according to a copy of the agreement obtained by the Post.
In court records filed Monday as part of a dispute between the team's owners, Synder's business partners called the woman's account "a serious accusation of sexual misconduct."
According to the agreement, the employee made "certain allegations" in 2009 and was later fired for cause.
"The agreement, which was signed on July 22 of that year by an attorney on behalf of Snyder and two other team executives, did not describe the nature of the allegations. In the agreement, neither Snyder nor the team acknowledged any wrongdoing," the Post reports.
The newspaper said details of the agreement it reviewed align with a settlement that surfaced that the NFL is conducting into sexual harassment with Washington's organization.
Snyder and the team declined to comment to the Post about the settlement or allegations. NFL spokesman Brian McCarthy also declined a request for comment on whether the league was aware of the settlement or allegations.
The woman did not respond to a request for comment and her attorney, Brendan Sullivan, declined to comment.
In July, Snyder hired attorney Beth Wilkinson following a report from the Post that included 15 former female employees of the team describing their experiences with sexual harassment within the organization. A month later, the Post published another report alleging a former senior executive instructed employees to create a behind-the-scenes video for Snyder, featuring outtakes of partially nude team cheerleaders from a 2008 team swimsuit calendar shoot. Snyder later denied the allegations.
Between its two stories, The Post interviewed 40 female employees about being sexually harassed in the workplace.
In August, the NFL took over Wilkinson's investigation.
On Nov. 9, David Donovan, Washington's former general counsel, sued Wilkinson to try to halt her from publicly releasing information related to a 2009 confidential settlement. Donovan dropped the suit, but a judge ruled that some documents should be made public. Since then, Washington Football Team lawyers have proposed redactions that would keep details of the settlement private.