Ireland suspended all government assistance to Kampala last month after an investigation by Uganda's auditor general found that millions of euros in aid had been funnelled into private accounts linked to the premier's office.

Two senior Ugandan officials are facing prosecution, while 17 have been suspended without pay while investigations continue, Gilmore said in a statement.

"I have received assurances from the highest level in the government of Uganda that they will repay in full the four million euros in Irish aid funding which was misappropriated by corrupt officials," the foreign minister said.

"It is my sincere hope that these actions indicate a renewed determination on the part of Ugandan authorities to tackle corruption, which is an affront to Ugandan citizens and the citizens of countries such as Ireland who have supported the country through very difficult times."

Irish officials travelled to Kampala last month to investigate the fraud after a probe by Uganda's auditor general found significant financial mismanagement by the prime minister's office in relation to an aid programme, Gilmore said.

The Peace, Recovery and Development Programme for Northern Uganda, set up in 2007 to rebuild the region after decades of conflict, was funded by Ireland and other donors including Norway, Sweden and Denmark.