In a June 26, 2026 letter addressed to Inspector General of Government Justice Aisha Naluzze Batoro, Museveni directed that Engineers Edwin Raymond Kiyaga, Dickens Ahimbisibwe and Patrick Muleme be suspended from duty pending investigations into what he described as the embezzlement of funds for the 23-kilometre expressway and its 20-kilometre access roads.
The President also directed that Bageya step aside for the duration of the investigations, with Under Secretary Barbara Namugambe appointed acting Permanent Secretary.
The letter follows reports that the President had ordered senior ministry officials to proceed on leave as investigations into the project gathered pace.
Mr Museveni said the government had initially secured Shs600 billion from the African Development Bank to finance the project in full, but despite only about 40% of the works being completed and that the entire amount being paid, the fund was used up.
"The government borrowed Shs600 billion from ADB to do the Expressway 100%. As of now only 40% of the work has been done but all the money was paid. What happened?" Museveni wrote.
The President accused engineers - including those he suspended - of altering the original road alignment to pass through land in which they allegedly had personal interests, thereby triggering fresh compensation claims despite the original route having already been surveyed and compensated.
"The corrupt engineers altered the route of the road and avoided the route that was already compensated for and charted a new route going through their own lands that needed fresh compensation. A road that was supposed to cost Shs600 billion is now being put at Shs1.3 trillion. These thieves must be destroyed," the President said.
Mr Museveni directed the Inspector General of Government to lead the investigations, assisted by State House Auditor General John Tumwiine.
"I therefore direct that Engineers Kiyaga, Ahimbisibwe and Muleme are suspended from duty and are investigated. You lead the investigations but my Auditor Tumwiine should also be involved," he wrote.
The suspension marks a dramatic shift from the Inspectorate of Government's position just weeks earlier.
In May, Deputy Inspector General of Government Anna Twinomugisha Muhairwe led an inspection of the Busega–Mpigi Expressway project alongside officials from the Ministry of Works and Transport following public concerns over delays, allegations that the contractor had abandoned the site, encroachment on the project corridor and questions over value for money.
Following the inspection, Muhairwe said the Inspectorate had been largely satisfied with the explanations provided by ministry officials and engineers regarding the project's progress.
"We are almost convinced with the explanation that they gave," she said after touring the site.
However, she raised concerns over illegal developments within the expressway corridor and inconsistencies in land valuation for affected property owners, warning that anyone found to have manipulated compensation processes would be held accountable.
At the time, ministry engineers explained that the project's increased financing reflected additional funding approved after construction stalled due to funding constraints.
Assistant Commissioner for Roads, Eng. Godfrey Bihemaiso, said the project's total financing had risen to approximately Shs1.3 trillion following the African Development Bank's approval of an additional €217 million (about Shs909 billion) in December 2025 to facilitate completion.
According to the ministry, the original contract was valued at about Shs547 billion, with the additional financing intended to cover project completion, outstanding compensation for project-affected persons and revised construction costs.
The Busega–Mpigi Expressway is a major transport corridor linking Kampala to central Uganda. The project includes a 23.7-kilometre four-lane expressway, more than 20 kilometres of access roads, four interchanges, toll plazas and supporting infrastructure.
It remains unclear whether the allegations cited by the President relate to the additional financing approved by the African Development Bank, changes in project scope, compensation claims, or other aspects of project implementation.
Neither the suspended officials nor the Ministry of Works and Transport had publicly responded to the President's allegations by the time of publication.