Witonze, a diplomat and politician, serves as the Chief Coordinator of the Patriotic League of Uganda (PLU) in the Greater Mpigi region.
He has also previously contested for election to the East African Legislative Assembly (EALA) and had again only recently showed interest in the by-elction for the same.
His appointment comes after the nomination of Dr Lawrence Muganga for the same position failed to secure approval from Parliament's Appointments Committee.
Muganga's vetting stalled after the committee raised questions regarding his citizenship status.
Officials familiar with the proceedings said the committee relied on a verification report from the Ministry of Internal Affairs indicating that Muganga was associated with Ugandan, Canadian and Rwandan citizenship.
According to sources, other ministerial nominees who faced questions over dual citizenship, including Adonia Ayebare, Calvin Echodu and Sharsti Kutesa Musherure, presented documentation showing they had initiated formal renunciation procedures with the relevant foreign authorities.
However, Muganga reportedly did not provide similar documentation during his appearance before the committee.
Although he disputed claims that he remained a Rwandan citizen, committee members insisted on documentary proof from the relevant authorities before recommending his approval.
The matter was subsequently referred back to President Museveni, who has now appointed Witonze to the position.
The appointment fills the vacancy in the Ministry of Internal Affairs following the unsuccessful vetting of Muganga and adds another Patriotic League of Uganda official to the Cabinet.