Coming just 10 days before Ankara is due to open EU membership negotiations the judgement prompted an unusually blunt condemnation from the Commission, which described it as "yet another provocation".
Last night efforts were under way to salvage the conference and bypass the legal ruling by holding it today at a new location.
But the judgement, which was condemned by the Prime Minister Recep Tayyip Erdogan, is a reminder of how far Turkey still needs to travel to guarantee freedom of expression.
Evidence of the power of the conservatives in Turkish society is likely to embolden critics of the country's EU membership bid. However Ankara's supporters say that internal reforms will only continue if Turkey is given the prospect of joining the bloc.
The row is unlikely to derail plans to start EU membership negotiations on 3 October in Luxembourg. The two leading sceptics over Turkey's EU membership, France and Cyprus, have been placated by language in a declaration stating that Ankara must recognise Cyprus before it joins the EU. Austria is isolated in its efforts to inject a new pledge that the negotiations could lead to a "privileged partnership" instead of full membership.
But the European Commission's spokeswoman for enlargement, Krisztina Nagy, said: "We strongly deplore this new attempt to prevent Turkish society from freely discussing its history. The timing of this decision the day before the opening of the conference looks like yet another provocation." She said the cancellation "illustrates the difficulties of Turkey, and in particular of the judiciary, to ensure effective and uniform implementation of the reforms". The killing of Armenians during the collapse of the Ottoman Empire remains a sensitive issue. A number of countries have recognised the massacres as genocide though that description is flatly rejected by Turkey.
The furore comes after a legal case against one of Turkey's most acclaimed writers, Orhan Pamuk who has been charged with insulting the country's national character. The trial, arising out of comments made on Turkey's killing of Armenians and Kurds, could lead to a prison sentence of up to three years.
The conference, which had already been postponed once, was scheduled to be held at Bogazici University. Aydin Ugur, president of Istanbul Bilgi University, said the gathering would take place this morning at Bilgi. He said the court's order was directed at two other universities, and had "nothing to do with Bilgi". But Laurent Leylekian, executive director of the European Armenian Federation, said: "We would be surprised if this kind of conference takes place in Turkey. There is no will in the government to open the Armenian file because this issues is deeply linked with the founding of the Turkish republic."
One EU diplomat described the ruling as "stupid" but added: "It is not going to cause a problem between now and 3 October. The EU has been very ready to criticise but not so ready to come through with its commitments." The Commission said it would note the issue in its annual report on candidate countries which is used as a yardstick of the membership preparation.Reuse content