Besigye was arrested at Jinja Road Police Station minutes after he had left Makindye court, which dismissed a case against him.
Besigye and Kampala Lord Mayor Erias Lukwago are accused of disobeying lawful orders given by Kampala South regional police commander Siraje Bakaleke during a meeting at Sharing Hall Nsambya in April 2015.
Gladys Kamasanyu Musenze, the Makindye Grade one Magistrate, dismissed the case on Monday saying prosecution has been promising to produce witnesses since the case started in May 2015 in vain.
Besigye was again re-arrested shortly after leaving court and his car towed to Jinja road police.
Police has not yet spoken on what Besigye is being charged with.