The charge may not be related to extradition as widely expected.
It may be for immigration-related offences, according to a report by Sahara Reporters.
Earlier today, Yoruba residents in Cotonou jammed the court to witness his arraignment.
They had protested on Wednesday demanding his release, as they said he had committed no offence.
Igboho was declared wanted by Nigeria’s DSS, a day after its operatives invaded his home in Ibadan, killed two persons and also destroyed his property.
The Yoruba Nation activist was on his way to Germany, along with his wife Ropo, when he was arrested at Cotonou’s Cardinal Bernardin International Airport.
He was said to be in possession of a forged Beninois passport.
The authorities of Benin Republic said they would dock him for the alleged forgery.