Kanu, a British citizen, is in jail awaiting trial and denies the charges against him. His lawyers told the court that the charges lacked merit and Kanu should be acquitted.
State prosecutors opposed the application and want Kanu to stand trial.
A three-judge panel of the court said a ruling would be made at a later date.
Kanu leads the outlawed Indigenous People of Biafra (IPOB), which has been pressing for the secession of a part of southeast Nigeria, home to the mainly Igbo ethnic group.
Nigeria's government views IPOB as a terrorist group and blames it on a spate of killings and attacks on government buildings in the southeast, which the group denies.
An attempt by Igbo separatists to secede as the Republic of Biafra in 1967 - the year Kanu was born - triggered a three-year civil war that killed more than 1 million people.