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.
The news of its failure to qualify comes at a time when Uganda's political will to fight corruption is facing stern tests both at home and abroad.
An inquiry into allegations of corruption in the multimillion dollar Global Fund against Malaria, Tuberculosis and HIV/Aids implicated several officials including the three ministers in the Ministry of Health but no action has been taken against them in spite of local and international pressure to do so.
The country has been disqualified from the latest round of HIV/Aids and malaria funding from the Geneva-based programme due to its failure to bring the culprits to book.
"There are substantial problems with Uganda's existing grants," a Global Fund official told our sister newspaper, the Daily Monitor, last week. "When there is an unsatisfactory past performance, a country must address to what extent a new grant will not suffer from the same problems."
Despite having a plethora of organisations to fight corruption, including a Cabinet Minister for Ethics and Integrity as well as an Inspector General of Government, Uganda's anti-corruption initiatives have largely proved to be paper tigers that have not led to arrests and prosecutions.
Although several commissions of inquiry have been held in the country over the past couple of years - into allegations of plunder in Congo, purchase of junk helicopters for the army, and into the police force - very few recommendations have been implemented and some implicated officials continue to enjoy senior positions in government.
Opposition MPs welcomed the news of Uganda's disqualification from the Millennium Challenge Account.
"My argument is that if we are corrupt, why should we beg for money that goes into a few corrupt people's hands?" Nandala Mafabi, a Member of Parliament from the opposition Forum for Democratic Change who heads the Parliamentary Accounts Committee, told The EastAfrican on Friday. "Our first task is to fight corruption."
Additional reporting by Herbert Benon Oluka