Weatherly, 50, spoke out in a statement to The New York Times in an article Thursday exposing how CBS paid Dushku a $9.5 million settlement following her allegations against Weatherly.
"During the course of taping our show, I made some jokes mocking some lines in the script. When Eliza told me she wasn't comfortable with my language and attempt at humor, I was mortified to have offended her and immediately apologized," Weatherly said.
"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," he former "NCIS" star added.
Dushku had a three-episode arc last year on "Bull," which stars Weatherly in the title role.
She seemed poised to become a series regular but was written off the show after confronting Weatherly about his behavior.
An investigation into CBS showed Dushku accused Weatherly of commenting about her appearance and making a rape joke and a remark about a threesome during her time on "Bull."
She entered mediation with CBS and was awarded a confidential settlement of $9.5 million.
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CBS confirmed it paid the sum to Dushku in the secret settlement.
"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 network said in a statement, according to CBS News.
The CBS Corporation board hired the law firms Covington & Burling and Debevoise & Plimpton in August to investigate multiple accusations of sexual misconduct against former CEO Leslie Moonves.
The firms were also told to examine "cultural issues at all levels" of the network.
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