A vaccination provider set up with money from the Bill and Melinda Gates Foundation has put on hold some $6 million earmarked for Sierra Leone after an audit showed misuse of previous funds, a document seen by Reuters showed.
The leaked letter from the GAVI Alliance dated November 15 2012 and addressed to Sierra Leone's health minister says an in-depth audit revealed "serious concerns of misuse of GAVI funds" totaling $1,099,640.
The GAVI Alliance, which aims to improve access to immunization in the world's poorest countries, was launched in 2000 with a $750 million grant from the Bill and Melinda Gates Foundation. It has disbursed more than $27 million to Sierra Leone's government since 2001.
Sierra Leone's acting Health Minister Tamba Borbor-Sawyer denied the GAVI letter was proof of foul play.
"The content of that document doesn't say the GAVI money has been defrauded ... It points out certain areas where there could have been some malfeasance," said Borbor-Sawyer, who took over management of the ministry earlier this year.
A GAVI spokesman said the irregularities, which included undocumented expenses, cash disbursements with no documentation and overcharged procurement costs, occurred from 2008 to 2011.
As a result, the organization froze the last disbursement of a current grant, worth $530,750, as well as a new two-year grant of $5,399,371 currently under final consideration.
Sierra Leone's government must now commit to reimbursing the misused funds and those found responsible for abuses must face administrative or legal proceedings before the grants will be unfrozen, the letter said.
After Sierra Leone's 1991-2002 civil war the West African state had some of the world's worst health statistics. In response donors poured in funds, in particular underwriting the introduction in 2010 of free healthcare for pregnant and nursing mothers, and children under five.
But allegations of corruption have dogged such efforts.
A 2011 investigation into the free healthcare program by human rights campaigner Amnesty International highlighted what it said was an "absence of any effective monitoring and accountability systems".
The new allegations brought by GAVI come six months after the United Nations appointed Sierra Leone's previous health minister, Zainab Hawa Bangura, as the secretary general's special representative on sexual violence in conflict.
Bangura began her tenure as health minister in January 2011 towards the end of the period in question.
She said she discovered upon taking office that donor funds for a number of projects had been paid into unsupervised bank accounts.
"At no time did I have direct oversight of these funds, nor was I ever a signatory authorized to disburse funds from these accounts," she said in a written statement.
Bangura said she raised her concerns with the finance ministry in mid-2011 and, when no action was taken, she brought the matter to the attention of President Ernest Bai Koroma.
Finance Minister Samura Kamara denied having been contacted by Bangura over the matter.
"The bottom line is that it is the ministry of health that has absolute responsibility ... We don't draw on these funds," he told Reuters.
Koroma's office said in a statement it remained committed to programs supported by GAVI and other development partners.
Koroma, who was elected in 2007 promising to clean up rampant corruption, won a second term in elections on November 17.