Chris Boyce, executive director of CBC-Radio, and Todd Spencer, executive director of human resources and industrial relations for English services, are on leave "until further notice," according to an employee memo distributed Monday.
Monique Marcotte will assume Spencer's responsibilities while Cindy Witten will take over for Boyce.
In November, the CBC said that Boyce, Spencer and director of network talk radio Linda Groen had conducted interviews with "Q" employees about Ghomeshi, the show's host.
Since that initial investigation, the CBC commissioned labour lawyer Janice Rubin to conduct an independent probe into how the public broadcaster handled the allegations of sexual violence against Ghomeshi.
CBC spokesman Chuck Thompson said that Boyce and Spencer's leaves were not voluntary but a "management decision." The departures were related to the Ghomeshi scandal, he said, but declined to elaborate further.
"As I'm sure you can appreciate, given our obligations of confidentiality to both Chris Boyce and Todd Spencer, we won't be making any further comments," Thompson said in a telephone interview Monday.
Boyce declined to comment while Spencer could not immediately be reached.
In the memo, meanwhile, the CBC urged employee unity.
"I believe it's especially important that we remain supportive of all our workplace colleagues where they may need it and resolute in our professionalism and dedication to the important work that we do here on behalf of Canadians," read the note, attributed to CBC executives Heather Conway and Roula Zaarour.
"We recognize this is a difficult way to start off the year, but despite our current challenges, together we will get through this, and we do have a great future."
The CBC fired Ghomeshi in October after seeing what it called "graphic evidence" that he had caused physical injury to a woman. He is also facing five criminal charges — four counts of sexual assault and one of choking — stemming from alleged incidents involving three women.
Ghomeshi has admitted he engaged in "rough sex" but insisted it was always consensual.
He has been released on bail and his lawyer has said he will plead not guilty.