Barroso defended the treaty, saying the EU needed the charter, which EU leaders signed in December to address problems facing Europe, including climate change and rising fuel and food prices.
"The 'No' vote in Ireland has not solved the problems which the Lisbon
treaty is designed to solve," Barroso said.
Frank-Walter Steinmeier, the German foreign minister, described the result "a severe setback" but said Berlin would stick to its aim of putting the treaty into effect.
"The ratification process must continue," Steinmeier said in a statement
released during a visit to China.
"I am still convinced that we need this treaty, a treaty that makes
Europe more democratic, more capable of acting and more transparent," he said.
The Lisbon treaty was designed to replace the EU constitution after it was rejected by French and Dutch voters three years ago.
It needs approval by all 27 EU member states.
Rejection leaves the EU, whose leaders meet for a summit in Brussels late next week, facing a crisis similar to that which followed the 2005 Franco-Dutch rejection to the EU's original constitution.
The treaty was drawn up to replace the constitution, but as a mere reforming treaty it largely escaped the need for such unpredictable national referendums.
However, Ireland, uniquely among the 27 EU member states, was constitutionally bound to hold a vote.
So far 18 of the 27 nations have ratified the treaty.