"The decision at (the) Bucharest NATO summit should not put that future under question," the EU's Slovenian presidency said in a statement.
It called on Macedonia to "intensify reforms in order to meet the conditions necessary towards opening of (EU) accession negotiations later this year."
Macedonia wants to join both the EU and NATO, however its bid to join the 26-member North Atlantic Treaty Organisation alliance was blocked by EU member Greece in a long-running row over the right to the name Macedonia, which is shared by a northern Greek province.
Macedonia stormed out of Bucharest on Thursday in protest after Greece used its veto.
The EU presidency, which Slovenia holds until handing over to France for the second half of this year, called on the former Yugoslav republic "not to lose sight of its strategic national goal of joining the Euro-Atlantic integrations".
It said these were "essential for the country's future, as well as of great importance for the entire region".
Regretting the name row, the statement said talks should be resumed "without delay," amd commended Macedonia for its efforts to "pursue reforms, to contribute to regional stability and to build a multi-ethnic society".
Greek Prime Minister Costas Karamanlis invited Macedonia to fresh talks over its name hours after Greece used its NATO veto.
"Greece's goal is not to humiliate (Macedonia), but to bolster it as a country that is trying to stand on its feet," he said in a speech at the Greek embassy in the Romanian capital.
Macedonia's constitutional name is the Republic of Macedonia. Skopje wants this used in international relations, except with Athens, where a name acceptable to both parties would be found.