Officials will be able to avail of flights between Brussels and Dublin for a fixed rate of €49.99 for the first six months of the year.
This is expected to rake in significant savings -- although many diplomats who are more used to VIP treatment may not be best pleased by the cost-cutting measure.
The airline made the offer to the Government last September and after an initial row over whether Minister Lucinda Creighton had responded to it, an agreement has now been reached.
A meeting took place between the airline and an agency working for the National Procurement Service during which the details of the offer were clarified.
"The offer was agreed and is now available for booking through the Travel Management Services Contract," said Ms Creighton.
Under the proposal, diplomats would be able to avail of set fares of €49.99. The airline also promised a dedicated "presidency" helpline, more than 30 days' "credit" to the State, free flight changes and assistance desks at the airports. Baggage charges would apply as normal.
According to Ryanair. if it flew just 1,000 officials during the presidency it would save the Government €3.5m. Overall it is expected in excess of 15,000 official flights will be made between Ireland and Belgium by the end of June.
"The National Procurement Service has made Government departments aware of this offer to inform their decisions in relation to travel arrangements between Dublin and Brussels during Ireland's presidency of the European Union during the first half of 2013," the minister said.
The Government has been heavily criticised in recent days for splashing out nearly €250,000 on the development of a website for the presidency, which begins on January 1.
The Department of An Taoiseach hired Terminal Four Solutions Ltd to operate the site. The cost of the contract was €244,741.71
The Department of the Taoiseach has confirmed a website design company, had been awarded a contract for professional services in relation to the EU presidency 2013 website.
A spokesperson has defended the cost, saying: "The website is the key communications tool for the Irish presidency of the EU. With over 2,500 pages on the site, eu2013.ie will be the primary source of information for all of our high level meetings held in Ireland and Brussels."