The Commission says the meeting was postponed until September to give the pro-Western government in Kyiv more time to implement political and financial reforms.
The delay also comes after voters in the Netherlands recently rejected an association agreement between the EU and Ukraine. That decision is due to be debated by the Dutch government in the coming weeks.
However, the Ukrainian President Petro Poroshenko still plans to hold a meeting with European leaders this June to discuss the current situation in the country.
The meeting, with European Council and Commission Presidents Donald Tusk and Jean-Claude Juncker is expected to discuss the Minsk agreement and elections in Donbass, the eastern part of Ukraine, which has witnessed most of the bloodshed in the bitter conflict.
News of the postponed summit comes after the Commission last week formally backed visa-free access for Ukrainians to the EU, opening the way for member states and Parliament to debate the proposal.
The executive said that Ukraine's government, which has made visa-free access a key political goal, has now carried out all the necessary reforms to win Brussels' backing.
These included a series of anti-corruption measures and stepped-up efforts against organised crime and border security.
European Parliament President Martin Schulz, speaking recently, said that "cooperation with Ukraine is essential and our solidarity should not be questioned".
Meanwhile, a Ukraine opposition parliamentarian has appealed for a new investigation to look into the events that led to the deaths of 48 people in Odessa, Ukraine two years ago.
Mykola Skoryk, a member of the Verkhovna Rada, said a thorough and independent inquiry was needed to establish the causes of the violence which culminated in a fatal fire at a trade union building in the Black Sea port.
The events played a key role in the unfolding violence further east, where Russia-backed separatists rose up against Ukrainian authorities.
Skoryk, who was in Brussels on Wednesday to lobby MEPs and the Commission to push for an investigation, was critical of the slow progress and incompetence of the official inquiry into the clashes between pro-Russian and pro-Ukrainian supporters.
The MP, who opened a photographic exhibition at Brussels press club, also welcomed moves to introduce visa-free travel for Ukrainians to Europe and called on the European Parliament to give its approval as soon as possible.
Over two years after the Euromaidan mass protests resulted in removing President Viktor Yanukovych from power, Ukraine is still at a crossroads between war and peace, between corruption and reform.
The entry into force of the EU-Ukraine free trade area on 1 January 2016 was seen as a milestone in relations between the two entities.
However, the conflict in the east of the countries, which has led to the deaths of over 7000 people, shows no sign of abating.