"I won't be surprised if al Qaeda or one of its affiliates ... were behind the attack because al Qaeda today definitely don't want to be upstaged by ISIS," Soufan told "CBS This Morning" Friday.
Gunmen stormed the luxury Radisson Blu Hotel in the capital city of Bamako Friday, taking 170 guests and staff as hostages.
Newly released ISIS propaganda videos threatening New York City and Washington are stirring fears of attacks on U.S. soil, similar to last week's carnage in Paris. But Soufan said al Qaeda also poses an imminent threat.
"ISIS may be stateless but the state of al Qaeda is very strong and we have to remember, ISIS came out of al Qaeda," Soufan said. "Al Qaeda is a poisonous tree and ISIS is just a branch of that tree. ISIS is a symptom of the disease, al Qaeda is the disease."
In 2013 France intervened to help Mali gain back control from al Qaeda-linked militants. But al Qaeda has also extended their network with affiliates operating in Syria, Yemen, Algeria, Tunisia and Libya. According to Soufan -- who was a key figure in the FBI's investigations of the terror group before and after 9/11 -- al Qaeda is now "way stronger" than it was on 9/11, when they had just 400 members.
Soufan also discussed important developments following last week's carnage in Paris over recent days. French prosecutors confirmed Thursday that Abedelhamid Abaaoud, the alleged ringleader of the Paris attacks, was killed in a police raid in Saint-Denis. Soufan said police were also able to disrupt more potential terror attacks.
"French sources tells us that were maps for the Charles de Gaulle airport, for the defense district in Paris, they found explosives, they found weapons," said Soufan.
While Soufan said these developments offered "some sense of closure," he said there "are a lot of things to be done" and threats remain high in Paris.
"Look at the network that conducted this attack. This network is not only a network in France - it's also in Belgium," said Soufan.