"If we're left as the only country that has not ratified the treaty, it will obviously raise questions. We're in uncharted waters," he said.
Ahern said he expected all other 26 EU members to ratify the Lisbon treaty through their national parliaments by the end of this year.
This would leave Ireland, the only member to put the document to a national vote, diplomatically isolated but nonetheless wielding the power to prevent the treaty from becoming law and forcing a period of renewed negotiations.
At the major ballot-counting centre in Dublin, Brian Lenihan, the finance minister, struggled to speak to reporters as anti-treaty activists drowned him out with songs and chants of "No!".
The outcome appears likely to throw the EU into renewed diplomatic turmoil and fuel cries across the continent for more democratic accountability.
The Lisbon treaty was painstakingly negotiated following the failure of the EU's proposed constitution, which French and Dutch voters rejected in 2005.
Both documents sought to reshape EU powers and institutions in line with the bloc's rapid growth in size and population since 2004.
The reforms included strengthening the roles of the EU's president and foreign policy chief, reducing the areas where individual nations could veto policy changes, and increasing the powers of the European parliament to scrutinise EU laws.
Ireland views itself as a pro-EU state that has broadly benefited from 35 years of membership.
Yet, anti-EU activists said voters clearly do not trust their political elites, whether in Dublin or Brussels.
"This is a huge rebuff to the political establishment. It shows there is massive distrust among ordinary working people," Joe Higgins, the sole Socialist party member in the Irish parliament said.
"People felt a convincing case for the treaty had not been made, and they felt hectored and bullied into supporting it while the wool was being pulled over their eyes," Richard Boyd Barrett, leader of People Before Profit, a left-wing pressure group said.