Speaking in a press conference in Khartoum on Friday, Lt Gen Omar Zain al-Abidin declared that "Bashir will be tried in our judicial system" while the military council is in control of the country.
This appears to temporarily put to rest questions about the prospect of Bashir facing trial at the International Criminal Court (ICC), which indicted him twice for crimes against humanity and war crimes in the western region of Darfur.
al-Abidin pointed out that this may change when the country reverts to civilian rule.
Mr. Bashir still faces war crimes and crimes against humanity instituted by the ICC.
While on trips abroad Bashir who ruled Sudan for thirty years, had dodged several attempts by the ICC to arrest and hand him over to the court.
al-Abidin said the military council is detaining the former ruler at a safe location, while a case against him is being prepared by state prosecutors.
Reacting to questions about the heavy handedness by pro-Bashir security forces on unarmed protesters al-Abidin said: "We will have zero tolerance for those who kill citizens".