CBS entered a new stage of turmoil on Wednesday with the ouster of the longtime executive producer of “60 Minutes,” its flagship news brand, amid a cascading scandal over sexual misconduct that days ago ended the career of the network’s chief executive, Leslie Moonves.

Jeff Fager, who was only the second person in 50 years to oversee “60 Minutes,” was fired for sending a text message that threatened the career of a CBS reporter, Jericka Duncan, who was looking into allegations of sexual harassment leveled against him and Mr. Moonves.

The president of CBS News, David Rhodes, told staff that Mr. Fager’s departure was “not directly related” to those allegations of sexual harassment, which Mr. Fager has denied. But the network said the producer had violated company policy.

It would be hard to overstate Mr. Fager’s power inside CBS’s news division, where he succeeded the legendary producer Don Hewitt in overseeing “60 Minutes.” Some members of the show’s staff were livid on Wednesday during a contentious meeting with Mr. Rhodes at the show’s Manhattan office.