The Irish government has received assurances from the Ugandan government that it will be paid back four million euros in misappropriated aid.
Joe Costello, Ireland's Minister of State for Trade and Development, has told RFI a "thorough investigation" is taking place, which will determine if the scandal implicates the highest levels of Ugandan government.
"There's a trail for the money," says Costello. "If that leads to the prime minister then so be it. But at the present time we have no information that the prime minister was aware of what the situation was."
Uganda's Prime Minister Patrick Amama Mbabazi has denied any knowledge of the missing development money. Two officials from the PM's office are facing charges, while another 17 have been suspended without pay pending further investigation.
Costello is certain the Irish aid money will be paid back. Although it is still not clear when that will happen, or whether that will be paid in a lump sum or instalments.
He says there has been an "absolute commitment", but it has not happened yet because the "actual detail of it hasn't been ironed out".
Ireland has been funding Uganda since 1994. Its development aid focuses on education, the fight against HIV/Aids, governance and poverty action. Ireland had been set to provide 16 million euros this year.
The four million euros involved in the fraud was part of a bigger package of funding from Ireland, Denmark, Norway and Sweden. A report published by Ugandan's Auditor General in October found that 12 million euros in aid had been transferred to unauthorised accounts linked to the office of the Ugandan PM.
"We will want to see what the outcome of the investigation is and what the outcome of the prosecutions are before we return to providing funding for Uganda," says Costello.
It is not the first time there have been concerns about Irish aid to Uganda and issues surrounding alleged corruption.
In July 2009, an Irish government parliamentary sub-committee on Official Development Assistance was assured that funds were not going missing as a result of corrupt practices, according to an Irish newspaper.
While in March 2002 the Irish Times reported an Irish minister as saying that aid would not be withdrawn from Uganda despite the murder of an Irish priest and corruption issues.
Costello, however, is certain that previous issues with alleged corruption were linked with Uganda's difficult past.
"Uganda is a country that has come out of enormous turmoil and civil war," he says. "We have put together a very strong audit and evaluation mechanism."
There are also questions about a possible conflict of interest between Irish Aid's Ugandan aid and Tullow Oil's operations in Uganda.
Coincidentally, Uganda had taken back an oil exploration block jointly owned by Tullow Oil, China's CNOOC and Total SA after their license expired, as reported on 24 October. Officials from Ireland flew to Uganda to investigate the misappropriation of aid funds on 25 October, according to Irish newspapers.
When asked whether oil and gas exploration company Tullow Oil's interests in Uganda came up during discussions of the suspension of Irish aid to Uganda, Costello replies, "no".
"Our aid is not tied in any way. So there is no direct relationship between Irish Aid and Tullow Oil," he says.
Tullow Oil's Chief Executive Officer, Aidan Heavey is on the board of the Irish enterprise charity Traidlinks, which is supported by both Irish Aid and Tullow Oil.
The Anglo-Irish oil firm, founded by Heavey in 1985, has a number of major projects in Uganda having drilled over 50 wells since 2006. At the same time Traidlinks, which says it aims to help developing countries by "inspiring, supporting and promoting enterprise", has two offices in Uganda with 11 staff members.
Costello denies that any such conflict of interest exists. Instead he assures Irish taxpayers that "at every level there is recognition" that aid is being provided for the Ugandan people
He says those responsible for the aid fraud will be bought to justice. This episode should neither stop Irish aid from helping Ugandans in need, or force Irish taxpayers to reconsider the money they are shelling out.
"This should be a very strong lesson," Costello says. "There must be a total clampdown on any corrupt behaviour by the people in authority that would prevent the aid, on the one hand, going to the people its intended to. But also could question governments as to whether or not it is appropriate to send that aid if there is that type of behaviour taking place at high levels of authority," he adds.