The Victoria University Vice Chancellor has refuted claims saying that he is not a Ugandan.
A passport that belongs to his mother has also been released to show that he has Ugandan relatives.
In a media interview earlier in the year, Dr Muganga said he was a Ugandan from Greater Masaka area and had lived and studied in the country up to university.
According to him, he visited Rwanda to help companies there build different capacities, before getting a scholarship to attend graduate school in Canada.
Last week, he was being held on allegations of espionage.
“He holds a foreign passport and has been working in Uganda illegally. His wife also has a Rwandan passport. They are in the country illegally,” Uganda People’s Defence Forces (UPDF) spokesperson Brigadier Flavia Byekwaso said.
Dr Mugaga was later released on Friday night and received by Rajiv Ruparelia, the Managing Director Ruparelia Group of Companies.