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"We value our partners and are working with them to address their current concerns about the O'Reilly Factor," Paul Rittenberg, executive vice president of sales, said in a statement provided to Business Insider.
Rittenberg added: "At this time, the ad buys of those clients have been re-expressed into other FNC programs."
By Tuesday afternoon, more than a dozen companies had pulled advertisements for O'Reilly's show, the highest-rated cable news program on television.
The Times' investigation into O'Reilly's conduct found that complaints against the host included lewd comments and unwanted sexual advances.
O'Reilly has denied that there is any merit to the allegations against him.
Last week, the embattled host hired crisis-communications expert Mark Fabiani, who released a statement to The Times on behalf of O'Reilly.
"Just like other prominent and controversial people, I'm vulnerable to lawsuits from individuals who want me to pay them to avoid negative publicity," the statement said. "In my more than 20 years at Fox News Channel, no one has ever filed a complaint about me with the Human Resources Department, even on the anonymous hotline."
The statement concluded: "But most importantly, I'm a father who cares deeply for my children and who would do anything to avoid hurting them in any way. And so I have put to rest any controversies to spare my children."
Sonam Sheth contributed to this story.