The transfer of Lt. Ersie Joyner III is "routine" and is being done as part of the regular transfer of top department officials, Thomason said.
Thomason said Sgt. Brian Medeiros, who is being promoted to lieutenant, will now head the homicide division.
In another move that will take effect on Saturday, Lt. Johnny Davis will move from patrol to training, Thomason said.
"We move lieutenants around all the time," Thomason said.
He said a court settlement that resolved a police abuse case recommended that chiefs move lieutenants around every few years.
Thomason said the department also believes that it's good to move lieutenants around so they are well-rounded in case they move up the ranks.
"We don't want people who are stuck in one thing," Thomason said.
He said Joyner is in line to be promoted to captain.
Bailey, 57, was shot to death in Oakland on Aug. 2, 2007, as he was walking from his home to his job as editor of the Oakland Post.
Your Black Muslim Bakery handyman Devaughndre Broussard, 21, is accused of murdering Bailey and is scheduled to go on trial early next year.
But Oakland police, including, Joyner, have been criticized for not being aggressive enough in questioning Your Black Muslim Bakery leader Yusuf Bey IV, 22.
Broussard's attorney, LaRue Grim, has alleged that Bey ordered Broussard to kill Bailey because Bey was upset that Bailey was writing an article about the bakery's financial problems.
But Bey hasn't been charged and Broussard is the only defendant in the Bailey homicide.
However, Bey is in custody for a separate case in which he and several associates are accused of kidnapping and torturing two women in Oakland in May 2007 as well as several other cases in several different counties.
Bey also is awaiting sentencing for his no-contest plea on July 30 to eight felony counts for leading a group of bakery associates who vandalized two West Oakland liquor stores on Nov. 23, 2005.