Kenya received passing grades in several areas, including political rights, spending on primary education, trade policy, and inflation.
But a public row between Attorney General Amos Wako and the director of the Kenya Anti-Corruption Commission (KACC) Aaron Ringera over the competence of investigations and evidence in five cases has left doubts over the government's commitment to tackling the vice.
Coming under a barrage of criticism over the pace at which it was conducting investigation into the Anglo-Leasing scandal - the biggest fraud to be uncovered under President Mwai Kibaki, who came to power in 2002 pledging to run a clean administration - the KACC sent five files involving Cabinet ministers to the AG.
After two weeks, Mr Wako returned the files and publicly pointed out shortcoming in both the quality of investigations and evidence gathered.
The Commission responded immediately, pointing out that issues raised by the AG had been answered, but Mr Wako maintained the queries he had raised "could have been noticed even by a first year law student."
In Uganda's case, it is also disqualified on the corruption count. It was given other failing marks on political rights, enrolment of girls in primary education, and the cost of starting a business.
Like Kenya, however, Uganda would have been deemed eligible for the programme had its corruption indicator been favourable.
Kenya and Uganda are among 11 countries earlier placed in a threshold grouping that enables them to consult with US officials about how to meet millennium aid eligibility criteria. But unlike several threshold countries, the East African neighbours have not yet completed formal agreements with the Millennium Challenge Corporation on how to proceed towards eligibility.
Tanzania did win approval of its threshold proposal last year. Tanzania has also again received a passing grade on the corruption indicator and all the other criteria included in the "ruling justly" category. It was given a failing score in regard to health expenditures, girls' enrolment in primary schools, and days needed to start a business.