The Foreign Affairs Minister Eamon Gilmore has sent an audit team from Ireland to the capital Kampala to try and secure the return of the funds.
Ireland gives around €33 million each year towards aid projects in Uganda.
Around half of that is administered by the Ugandan government.
All aid stopped
Today it has emerged that a payment of some €4 million of Irish taxpayers money was lodged into an unauthorised account in Uganda.
The Foreign Affairs Minister Eamon Gilmore has this afternoon ordered that all aid to the Ugandan government be stopped.
Weapons buying programme?
He has also sent a team from Ireland to try and get the money back.
When asked if the money from Ireland could have been used as part of the Uganda weapons buying programme the Tánaiste said the audit team would be tasked with finding that out.
