SAN FRANCISCO — The Tor Project, a nonprofit digital privacy group, announced on Wednesday that an internal investigation had confirmed allegations of sexual misconduct against a former employee who was the public face of the organization.

The group, which has risen to prominence at a time of controversy over government surveillance, had been grappling for months with allegations against Jacob Appelbaum, a top figure in the internet privacy debate. Mr. Appelbaum resigned from the Tor Project in May.

The allegations have divided the internet privacy community and have raised questions about management of the project, which promotes the use of software that helps internet users mask their online identities and whereabouts.

One result was the replacement of the group’s entire board this month.

On Wednesday, the Tor Project said that a seven-week investigation into the allegations involving Mr. Appelbaum determined they were accurate. Mr. Appelbaum, who is also the only American member of the anti-secrecy group WikiLeaks, has denied the allegations and has said they are “entirely false.”