Dan Oola Odiya, was arrested Wednesday evening by plain clothed police officers near Amigos bar in Gulu municipality.
He was first taken to Aswa Region police headquarters and then the 4th Division Army barracks.
Patrick Jimmy Okema, the Aswa Region Police spokesperson, later told Uganda Radio Network, Odiya was detained at Gulu Central Police Station.
The Police say they have intelligence linking the official to a serious crime.
Sources says Odiya will be charged with treason for mobilising the youth to join a rebel group that is yet to be named by the police.