The removal of Staff Lieutenant General Mohammed Ridha may indicate that security forces will take a harder line against demonstrators who are expected to protest later this week, AP reported.
Angry demonstrators broke into the Green Zone and stormed parliament Saturday in an unprecedented security breach.
Iraqi Prime Minister Haider al-Abadi issued an order "for the relief of special forces division commander Mohammed Ridha," who will be replaced by Major General Karim Aboud al-Tamimi, a statement from Iraq's Joint Operations Command said.
The removal of Ridha may be a sign that security forces that stood by as demonstrators broke into the Green Zone will now take action against them if they attempt to do so again.
Demonstrators are expected to protest Friday and may attempt to re-enter the Green Zone, which is home to Iraq's main government institutions as well as various embassies.
Angry protesters broke into the area after lawmakers again failed to approve new ministers proposed by Abadi.
Abadi has called for the current cabinet of party-affiliated ministers to be replaced by a government of technocrats.
But his efforts have been opposed by some political parties that rely on control of ministries for patronage and funds.