Ibrahim Salami, one of the lawyers representing Sunday Adeyemo, Yoruba Nation activist better known as Sunday Igboho, says new charges were brought up against his client on Monday.
Salami said Igboho came to Benin through a back channel and the judge said he might have had some criminal association while in Benin, calling for further investigation on his entrance and stay in the country.
The lawyer said there were nine lawyers who represented Igboho at the Beninese court, and they were all shocked to see how the case turned out.
In an interview with the BBC, Salami said if Igboho wanted to cause problems in Benin, he would have stayed longer in the country, but he was willing to leave the country less than 24 hours after coming to Benin.
He said the court eventually ruled that Igboho be held in a Beninese prison until the investigation is concluded.
A final judgment has not been made by the Beninese court sitting in Cotonou, but the lawyers are now seeking to bail Igboho pending the investigation.
He said the case started with fighting off extradition to Nigeria, but ended as a case of Sunday Adeyemo versus the Benin Republic.
Igboho was sent back to prison by the court, following a 13-hour hearing at the Cotonou court of appeal.
Igboho and his wife, Ropo, were arrested at an airport in Cotonou last week and detained at the request of the Nigerian government.
His lawyers requested the release of his wife on the grounds that she had committed no offence against the Nigerian state.
On Thursday, the court answered the prayers and ordered her release and a return of her passport. Igboho was taken to detention, where he has been up until Monday.
The charges against the Yoruba Nation activist border on arms smuggling, inciting violence, and calling for a secession of the Yoruba from the Nigerian state.
Igboho and his lawyers have denied all allegations levelled, until the fresh allegations bordering on illegal entry and criminal association was presented before the third judge in court on Monday.