Lawrence Muganga, a vice-chancellor at Victoria University, was stranded on the streets of the capital, Kampala.
Those who saw his arrest on the exchange said they thought he was being treated as a close ally of the Rwandan military, which has not yet had a good relationship with Uganda.
Ugandan military spokesman Brigadier Flavia Byekwaso said Muganga had been arrested for making noise theft and living in the country illegally.
Earlier this year, Muganga led a campaign to demand that Rwandans living in Uganda be called Brethren, as he says they have been persecuted and some of their legal status as an identity card because they are considered foreigners.
Muganga, he was born in Uganda, where his parents fled to refugee camps after leaving Rwanda to escape mixed ethnic genocide in the 1950s.