Chakwera said Nundwe firing was unconstitutional and the former regime abused its powers.
The President said soon he will be calling for the Security Council meeting to discuss on the position of his deputies.
Former Malawi’s President Peter Mutharika fired Nundwe, replacing him by Andrew Lapken Namathanga.
Meanwhie, Nundwe says his re-instatement to the position provides a window to continue from where he left in serving the nation.
He told local media that " I will finish my mission...to ensure the military serves the interests of the people."
Nundwe successfuly led the MDF in controlling violent demos across the country after the Police lost the trust of Malawians during the nine months elections dispute case.
Nundwe's re-instatement comes nearly five months after he was relieved of his duties by former president Professor Arthur Peter Mutharika.
"God is great. I was removed for doing my job. I am happy that I am back. I will continue to serve from where I stopped serving Malawi," he was quoted by the Nation.