The planned university conference, entitled Ottoman Armenians of an Empire in Decline, was to have opened on Friday. It already had been aborted once after Justice Minister Cemil Cicek in May branded such discussion as "treason" and a "stab in the back of the Turkish nation".
Thursday's court order followed a complaint by a non-governmental organisation of lawyers opposing the three-day event.
"We received an order from the court, asking us to supply the court with information on the case within 30 days and ordering us to suspend our activities during this period," Nukhet Sirman, an academic on the organising committee, told AFP.
Sirman said the organisers had received a telephone call from the governor of Istanbul, Muammer Guler, "who apologised but said he had to implement the law".
The nature of the complaint against the conference was not immediately clear.
Armenians say 1.5 million of
their kin were killed
Cicek's outburst raised eyebrows in European diplomatic circles about Ankara's commitment to democratic reforms, a requirement for the 3 October negotiations over its adhesion to the European Union.
Prime Minister Recep Tayyip Erdogan then distanced himself from the minister's remark, calling it "a personal statement" and said he encouraged researchers to carry out their work.
The Armenian massacres constitute one of the most controversial periods of Turkish history.
Armenians claim up to 1.5 million of their people were slaughtered in mass killings under the Ottoman Empire, forerunner to the present-day Turkish republic.
Ankara categorically rejects claims of genocide and argues that 300,000 Armenians and at least as many Turks died in civil strife during World War I, when the Armenians took up arms for independence in eastern Anatolia and sided with Russian troops invading the crumbling Ottoman Empire.
The issue has taken on increased importance as some European politicans have pressed Turkey to address the genocide claims in what Ankara sees a politically motivated campaign to impede its bid to become a member of the European Union.
Erdogan previously said he
encouraged academic research
Much to Ankara's anger, the killings have already been acknowledged as genocide by a number of countries, including France, Canada and Switzerland.
"Our aim is simply to bring together Turkish intellectuals in an appropriate setting for the discussion of a subject that until now has been carefully avoided," said historian Edhem Eldem, who was to have participated in the conference.
"It is not a question of setting up a tribunal or reaching definitive conclusions," he told AFP.
Several nationalist groups expressed outrage over the planned conference. The Hur party called it a "perfidy" and the small left-wing Workers' Party called for demonstrations outside the Bogazici University, where the conference was to have been held.
The meeting had been expected to bring together about 60 researchers, including critical intellectuals, to examine events in eastern Anatolia between 1915 and 1917, as well as genocide denials made by the Turkish state since that time.
Any questioning of the official line that a genocide did not occur has proved dangerous to writers and intellectuals.
"Our aim is simply to bring together Turkish intellectuals in an appropriate setting for the discussion of a subject that until now has been carefully avoided"
Historian Edhem Eldem
Orhan Pamuk, the widely translated author of such internationally renowned works as The White Castle and Snow, is set to go on trial in December for telling a Swiss newspaper in February that "one million Armenians were killed in these lands and nobody but me dares to talk about it".
Pamuk said he subsequently received several death threats and a local official ordered the seizure and destruction of his works.
In Switzerland, where holocaust denial is a crime, the leader of the Workers' Party, Dogu Perincek, is under investigation for calling the genocide claim "a historical lie".