The Kenya Medical Research Institute (Kemri) has sent three senior managers on leave as it starts investigations into claims of financial mismanagement after the budget of more than $80 million was depleted prematurely, threatening key research projects and putting more than 1,000 members of staff at risk of losing their jobs.

The EastAfrican has learnt that the director for the Centre for Global Health Research at Kemri, Dr John Vulule, under whose docket the affected programmes fall, is among those sent on leave. Dr Pauline Mwinzi will take charge of the programmes in an acting capacity.

Kemri has been in the spotlight after it emerged that despite receiving 92 per cent of the current year’s budget for programmes it runs jointly with the Atlanta-based Centres for Disease Control (CDC), it had spent nearly all the money with less than a month’s operating cost left in its account, and five months left in the budget period.

CDC has been collaborating with Kemri for 36 years now in conducting human health research in malaria, tuberculosis, HIV/Aids, schistosomiasis and other emerging and re-emerging infectious diseases.

These projects are covered under a Co-operative Agreement (CoAG) signed mutually between the two parties and runs for a period of five years on renewable terms. The current CoAg covers the period 2010-2015. The CoAg projects are based at the Kemri Centre for Global Health Research in Kisian, Kisumu.

Kemri corporate affairs manager Davis Mgoji said the organisation’s board had instituted investigations into the matter and would issue a statement once it had established all the facts.

“Several allegations have been made concerning commingling of funds belonging to the Co-operative Agreement (CoAg) programme. That’s the reason the board has initiated investigations,” Mr Mgoji said.

A fortnight ago, The EastAfrican reported about Kemri's financial mismanagement on the CoAg, which was exposed by a confidential document from the premier institution’s main donor, the Atlanta, US-based Centres for Disease Control (CDC). Kemri, however, said that despite the budgetary shortfall, all the research activities are on course.

“The CoAg programme activities are ongoing and if there is any shortfall on the budget, we will establish that once the investigations are completed. However, we expect additional funding from CDC, as has been the practice, to ensure that there is smooth running of the critical programme activities to August, 2015 when the CoAg is expected to end,” Mr Mgoji said.

However, it is understood that CDC is looking at emergency funding that would be used for specific projects.

CDC had requested Kemri to provide a “barebones” budget for activities that need to continue to avoid harm to patients and clinical trial participants. Such activities include HIV care and treatment. Some activities will need to continue to avoid loss of major investments.

“Within CDC Kenya, we are exploring funding options for the ‘barebones’ budget that will have to undergo review and approval from Atlanta,” the document stated.

However, Mr Mgoji would not admit or deny receiving such a request, saying that it is only after the investigation by the board that such information can be responded to.

The EastAfrican has learnt that CDC has requested financial accounts for these programmes for auditing.

“We want to state categorically, that CDC has not been denied access to any financial accounts for these programmes for audit purposes. Indeed, the CoAg accounts are audited annually by a competent professional firm appointed by both CDC and Kemri. These accounts are available for audit verification by CDC or any other party that may wish to access them,” Mr Mgoji said.

Kemri’s board of management held a meeting with the staff under the CoAg programme in Kisumu on Friday to reassure them about the impact of the financial challenges and the audit it would undertake.