The actress quit the hit show last year and took to Twitter in June, urging fans to stop asking about a possible return and revealing she was "terrified" of Harmon.
"I have nightmares about it," she wrote.
But, speaking to reporters at the Television Critics Association summer press tour, CBS Entertainment executive Kerry Kahl said, "I can't speak to what she's addressing in her tweets, but she did come to us a couple of years ago with a workplace concern and we immediately investigated it, and we resolved it to everyone's satisfaction."
"We are very happy to have her on the air again this year with us (for the show "Broke"), and I don't think she would be back with us if she had huge concerns."
The conflict between Perrette and her co-star allegedly began when Harmon started bringing his dog to the set in 2016, and an alleged biting incident occurred at the time.
Responding to comments the actress made as she exited the show in 2018, a CBS spokesman said: "Pauley Perrette had a terrific run on NCIS and we are all going to miss her. Over a year ago, Pauley came to us with a workplace concern. We took the matter seriously and worked with her to find a resolution. We are committed to a safe work environment on all our shows."