The military said Lieutenant Colonel Michael Browder, the commander of the unit was removed from his post "due to lack of confidence in his ability to command effectively."
Browder is not accused of committing any crime, but the two soldiers were under his command.
Last month, two other US soldiers were charged with the murder of three Iraqis.
Sergeant Michael Hensley and Specialist Jorge Sandoval were charged with the murder of three Iraqi nationals in three separate incidents.
They have also been charged with wrongfully placing weapons next to the bodies of the dead Iraqis, revealed after complaints from fellow soldiers led to an investigation.
The killings allegedly took place between April and June near the town of Iskandiriya, 50km south of Baghdad.
Hensley and Sandoval are currently being held in Kuwait.