He is now held at a high-security prison and will be questioned about the cash, sources said.
"The council is committed to give power to (the) people", Burhan said in his first interview on state television since taking power, after his predecessor stood down less than 24 hours after becoming military council chief following the ouster of long-time president Omar al-Bashir.
The source also confirmed Mr Bashir was under investigation, telling Reuters prosecutors would "question the former president in Kobar prison". He is wanted by the International Criminal Court for alleged genocide crimes in Sudan's Darfur region, but the military has said they intend to try the former ruler in Sudan.
Thousands of protesters who gathered outside army headquarters in Khartoum for a meeting to announce a civilian council they now want to take power.
Ahmed Rabi, leader of the SPA, said he and others behind the protest movement met the military council on Saturday.
So far, the SPA has been uncompromising in its demands, fearful of a military-led administration stuffed full of Mr Bashir's allies.
On Wednesday, Sudan's transitional military council ordered the central bank to review financial transfers since 1 April and to seize "suspect" funds, according to state news agency SUNA.
In another part of a widening crackdown created to remove remnants of Bashir's rule, the transitional military council (TMC) said it will retire all eight of the officers ranked lieutenant general in the National Intelligence and Security Service.
"The trial is a step that the military council wants to take to satisfy the protesters by presenting al-Bashir for trial", he said.
"We are not greedy at all to want to stay in power more than the time we agreed upon with the opposition parties".
Saudi Arabia and the United Arab Emirates said on Sunday they had agreed to send Sudan $3 billion worth of aid, throwing a lifeline to the country's new military leaders after protests led to the ousting of president Omar al-Bashir.
But while the council promised not to remove protesters from their sit-in, it has also called on them to stop unauthorised roadblocks and "let normal life resume".