Ukrainian President Viktor Yanukovich abruptly froze plans to sign the trade and reform deal last week, under pressure from Russia.
EU leaders have been trying to persuade him to change his mind.
The deal was planned as the highlight of a summit aimed also at building ties with other East European states.
But Lithuania's President Dalia Grybauskaite told the Agence France-Presse news agency that EU "arguments did not reach Ukraine president's ear and mind".
"So far we see that positions have not changed," she said.
And when asked how negotiations went, Polish Foreign Minister Radek Sikorski said: "They didn't. "It's over," he told The Associated Press.
Pro-EU protests are continuing in Ukrainian cities against the government's decision to back out of the agreement.
Mr Yanukovych has dismissed an EU condition for signing the agreement - that Yulia Tymoshenko, the former Ukrainian prime minister and opposition leader, be freed from jail.
He has requested more EU financial aid.
The dispute has increased tension between the EU and Russia, with Ukraine complaining it is becoming a "battleground" between the two.
EU leaders said in a statement that they "strongly disapprove" of Moscow's pressure on Ukraine not to sign - while Russian President Vladimir Putin accused the EU of "blackmail".
German Chancellor Angela Merkel, who is expected to have talks with Mr Yanukovych on Friday, said on arrival in Vilnius that she had "no hope" of the agreement being signed "this time".
"But the door is open," she added.
In other summit business, UK Prime Minister David Cameron raised concerns about the free movement of people in the EU.
Britain is planning to restrict access to welfare benefits for new immigrants from Romania and Bulgaria, when labour restrictions are eased in January.
The two-day event, billed as the third Eastern Partnership Summit, is being held in the capital of Lithuania, which currently holds the rotating presidency of the EU.
Initial political association agreements with Georgia and Moldova are due to be signed, as well as a visa agreement with Azerbaijan.
However, the centrepiece of the summit had been the association agreement with Ukraine.
Such agreements, which promote democratic values and economic co-operation, are seen as a key step towards EU membership.
On arrival in Vilnius, President Yanukovych met the President of the European Council, Herman Van Rompuy.
No details were given.
In a Ukrainian TV interview earlier, he accused the EU of offering his country an inadequate amount in loans to help reform the economy.
The EU has offered to lend 610m euros (£510m; $828) in macro-financial assistance, provided that Ukraine continues to meet the conditions of an IMF stand-by loan of 11.15bn euros ($15.18 billion), agreed in 2010.
Mr Yanukovych said Ukraine would need at least 20bn euros ($27.23 billion) a year to cover the costs of upgrading its economy to "European standards".
"For three years in succession they [EU leaders] have shown this candy in pretty wrapping to us," he added.
"We don't have to be humiliated like this. We are a serious country, a European one."
Defending the EU's offer, EU Enlargement Commissioner Stefan Fuele said:
"The Ukrainian economy needs huge investments but these are not costs. They represent future income, more growth, more jobs and more wealth.
"The only costs that I can see are the costs of inaction allowing more stagnation of the economy and risking the economic future and health of the country."
Prominent Ukrainian opposition politician Vitali Klitschko, who is also in Vilnius, said he hoped the agreement would be signed after all.
"We Ukrainians want the changes," the world boxing champion added.
"We want to live with the European family, with European rules, with Europeans' life standards."
The Ukrainian president has attacked EU demands to free Tymoshenko, saying:
"What does the European Union have to do with this? Is the European Union a court?"
In a message from her prison cell in Kharkiv, Tymoshenko called on EU leaders not to let her continued imprisonment block the association agreement.
"If Yanukovych takes a positive decision, I sincerely ask you [EU country leaders] to sign the agreement without any preconditions, including my release," she said in the message, read out by her daughter Eugenia.
Source: BBC News