According to The New York Times, Eliza Dushku was set to become a full-time cast member before then.
Weatherly, who appeared on NCIS for 13 seasons, allegedly made a rape joke and joked about having a threesome with her in front of other cast and crew members.
Weatherly has denied the claims, telling the New York Times: "During the course of taping our show, I made some jokes mocking some lines in the script. When Eliza told me that she wasn't comfortable with my language and attempt at humour, I was mortified to have offended her and immediately apologised.
"After reflecting on this further, I better understand that what I said was both not funny and not appropriate and I am sorry and regret the pain this caused Eliza."
CBS told Fox News in a statement Friday, "The allegations in Ms Dushku's claims are an example that, while we remain committed to a culture defined by a safe, inclusive and respectful workplace, our work is far from done.
"The settlement of these claims reflects the projected amount that Ms. Dushku would have received for the balance of her contract as a series regular, and was determined in a mutually agreed upon mediation process at the time."
