The European Union called the academic conference on Saturday a test of freedom of expression in Turkey, which is hoping to begin talks for membership in the bloc next month.
The academic conference had been cancelled twice, once in May after the justice minister said organisers were "stabbing the people in the back," and again on Thursday when an Istanbul court ordered the conference closed and demanded to know the academic qualifications of the speakers.
Heavy police presence
Police presence at the rescheduled conference was heavy, with 11 police buses and an armoured vehicle outside the venue, and dozens of officers in riot gear keeping hundreds of shouting protesters at bay. Some protesters pelted arriving panellists with eggs and rotten tomatoes.
Inside, the audience of more than 300 people was quiet and respectful, as only those invited by the organising committee and pre-approved members of the media were allowed past security.
The Armenian issue stirs deep passions among Turks, who are being pushed by many in the international community to say that their fathers and grandfathers carried out the first genocide of the 20th century.
Turkish academics have called
for a discussion of the killings
The issue has been a taboo for many years in Turkey, with those who speak out against the killings risking prosecution by a Turkish court. But an increasing number of Turkish academics have called for a review of the killings.
Stating that Turks may have committed genocide offends a large percentage of the Turkish people, who see the Ottoman Empire as a symbol of Turkish greatness, and the war that coincided with its collapse as a heroic struggle for national independence.
In a sign of the deep sensitivity of the subject, the panellists, all Turkish speakers, carefully avoided any emotional language during the first day of the two-day conference.
"Everyone waits for you to pronounce the genocide word - if you do one side applauds and the other won't listen," said Halil Berktay, programme coordinator of the history department at Sabanci University, speaking at the conference on Saturday.
Several governments around the world have recognised the killings of as many as 1.5 million Armenians in the late Ottoman Empire as genocide.
Turkey vehemently denies the charge, admitting that many Armenians were killed, but saying the death toll is inflated and that Armenians were killed along with Turks in civil unrest and intercommunal fighting as the Ottoman Empire collapsed between 1915 and 1923.
"This is something that's directly related to the question of what kind of country Turkey is going to be"
Organising committee member
After the conference was shut down on Thursday, Turkey drew condemnation from the European Commission, which said it deplored the decision and would make note of it in a progress report on Turkey to be released 9 November.
Organisers skirted the court order by changing the venue of the conference.
"This is a fight of 'can we discuss this thing, or can we not discuss this thing?'" Murat Belge, a member of the organising committee, said at the conference opening.
"This is something that's directly related to the question of what kind of country Turkey is going to be."
The court-ordered cancellation on Thursday was an embarrassment for the country's leaders, who are set to begin EU negotiations on 3 October.
Foreign Minister Abdullah Gul lamented that "there's no one better at hurting themselves than us," and sent a letter wishing the organisers a successful conference.
Prime Minister Recep Tayyip Erdogan also condemned the court's decision, saying it did not befit a democratic country.