Rwanda, which has been striving to rebuild itself following the 1994 genocide, was by far the least corrupt country in East Africa.
Rwanda and its neighbour Burundi were included in the East African Bribery survey for the first time.
Burundi was ranked as the most corrupt nation, dislodging Kenya, where a slight improvement was registered.
The survey measures bribery levels in the private and public sectors and was conducted between January and March this year.
Rwanda’s critics say corruption is so low because it is a police state
It is holding elections next month but opposition groups say they have been barred from taking part.
Transparency International said it was unable to produce a comparison of how Rwanda’s institutions fared because reports of bribery were so low – and no Rwandan organisation was included in the regional comparison.
It names the Revenue Authority in Burundi as the most corrupt organisation in East Africa, followed by its police force with Kenya’s police in third place.
East Africa’s common market came into force this month and is expected to boost trade across the five East African nations surveyed.
However, Transparency International warns that corruption threatens to hold back the common market’s full potential.
It notes that people often do not bother to report cases of corruption in the region.
For example, 93% of respondents from Uganda, which was listed as East Africa second-most corrupt nation, did not report the matter to any authority.
Since the genocide, in which some 800,000 ethnic Tutsis and moderate Hutus were killed, Rwanda’s government has acquired many admirers in the West for its efficiency.