Only Rwanda scored above the 50 point threshold.
East African countries continue to perform poorly in the fight against bribery and secret deals, the latest Corruption Perception Index by graft watchdog Transparency International (TI) shows.
The 2016 index ranks 176 countries perceived levels of public sector corruption and draws on data from the World Bank, the African Development Bank, the Economist Intelligence unit and other institutions.
Somalia has, for the 10th year running, been ranked as the most corrupt country in the world despite improving by two points to score 10.
The TI scale runs from 0 to 100, where zero means very corrupt and 100 very clean.
War-torn South Sudan is the second most corrupt globally with a score of 11.
Burundi is the third most corrupt in East Africa with a score of 20, followed by Uganda at 25, Kenya at 26 and Tanzania at 32.
Rwanda has, for the second year in a row, scored above the 50 point threshold having maintained 54 points.
The country also retained its status as the least corrupt in the region.
In the global rankings, Burundi was position 159, Uganda 151, Kenya 145, Tanzania 116 and Rwanda at 50.
Need for reforms
More than two-thirds of the 176 countries ranked scored below 50, with TI stating that deep-rooted reforms were needed globally to tackle increasing inequality and systemic corruption.
"The global average score is a paltry 43, indicating endemic corruption in a country's public sector," TI said in a statement.
"The lower-ranked countries are plagued by untrustworthy and badly functioning public institutions like the police and judiciary. Even where anti-corruption laws are on the books, in practice they're often skirted or ignored," it said.
In sub-Saharan Africa, Botswana maintained its status as the least corrupt with a score of 63, followed by Cape Verde at 59, Mauritius and Rwanda at 54 and Namibia at 52.
The five are the only African countries to have scored above 50, showing how entrenched corruption still is in the continent.
“Some other large African countries have failed to improve their scores on the index. These include South Africa, Nigeria, Tanzania and Kenya. South African President Jacob Zuma was in court and in the media for corruption scandals,” the watchdog said.
“Kenya – despite the adoption of a few anti-corruption measures including passing a law on the right to information (Access to Information Act 2016) – has a long way to go. President Uhuru expressed frustration that all his anti-corruption efforts were not yielding much. He may need new strategies as Kenyan citizens go to the polls in 2017,” TI added.
Cape Verde and São Tomé and Príncipe are the most improved African countries in the new index.
"Both countries held democratic presidential elections in 2016. It is no surprise that the independent electoral observer teams labelled the Cape Verde elections for 2016 as “exemplary”.
“In São Tomé and Príncipe elections held in July 2016 led to a smooth change of government, which is increasingly a challenge in the African region,” it concludes.
Denmark, New Zealand - the only two with scores of 90, Finland, Sweden and Switzerland made the top five globally.
But TI warned that even the top scorers cannot afford to be complacent.
"While the most obvious forms of corruption may not scar citizens' daily lives in all these places, the higher-ranked countries are not immune to closed-door deals, conflicts of interest, illicit finance, and patchy law enforcement that can distort public policy and exacerbate corruption at home and abroad," it said.