The conclusion of the trade and reform deal was planned as the highlight of a summit aimed also at building ties with other East European states.
Ukraine’s President Viktor Yanukovych is likely to face tough questions from EU leaders on why he stopped the deal, apparently under Russian pressure.
Viktor Yanukovych has requested more EU financial aid.
Pro-EU protests are continuing in Ukrainian cities against the government’s decision to back out of the deal.
Viktor Yanukovych has dismissed an EU condition for signing the agreement – that Yulia Tymoshenko, the former prime minister and opposition leader, be freed from jail.
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 Viktor Yanukovych on Friday, said Russia should not view relations between the 28-state bloc and ex-Soviet republics as a threat.
“We should overcome the ‘either us or them’ mentality,” Angela Merkel said.
“The Cold War is over.”
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.
The leaders are due to hold informal talks at a dinner on Thursday evening, with the official business of the summit to be conducted on Friday.
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.
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