The former host of CBC Radio's cultural affairs show "Q" was originally charged with seven counts of sexual assault and one count of overcoming resistance by choking.
Crown prosecutor Mike Callaghan said Tuesday that two sexual assault charges were being withdrawn because there was no reasonable prospect of conviction.
"We wish to be abundantly clear this determination is not a reflection of the truthfulness or credibility of any witnesses but rather a determination that specific allegations would not meet the legal burden of proof," Callaghan told Justice Rebecca Rutherford.
Outside court, Callaghan said the two charges involve two separate female complainants who are not involved in the remaining charges.
He said he had spoken with the two women, whose identities are shielded by a publication ban.
The CBC fired Ghomeshi, 47, in October after executives saw what they described as graphic evidence that he had physically injured a woman.
The one-time radio star has admitted to engaging in rough sex but said it was consensual. His lawyer, Marie Henein, has said he will plead not guilty to all charges.
The alleged assaults for which he was originally charged occurred between 2002 and 2008.
Callaghan also asked the court to treat one of the sexual assault charges as a separate matter, to be tried June 6 to 10, 2016.
The remaining charges will be tried Feb. 1 to 19, 2016, with pretrial motions to be heard Oct. 1 and 2.
Henein agreed to the dates, telling Rutherford the defence was "obviously anxious to have this heard in a courtroom before a judge."
Ghomeshi's $100,000 bail conditions require him to remain in Ontario and live with his mother.