Bells rang and the liturgy echoed from inside an Armenian church in eastern Turkey for the first time in nearly a century at a Sunday service symbolising Turkish efforts to overcome its troubled history with ethnic and religious minorities.

The Holy Cross church on Akhtamar island, a rocky outcrop in Lake Van, is one of the few visible remnants of the Armenian communities that were settled across eastern Anatolia until the Ottoman-era massacres and deportations of 1915, in which an estimated 1.5m died. Most Armenian churches were destroyed.

Turkey’s decision to allow worship one day each year at the church, which was opened as a museum in 2007, is a gesture of goodwill at a time when talks between Ankara and Yerevan to normalise diplomatic relations have stalled.

It is also part of a broader effort by the ruling Justice and Development party (AKP) to end the ethnic and religious divisions that have shadowed Turkey since the creation of the modern republic. The Greek Orthodox monastery at Sumela, near the Black Sea coast, was permitted one day of worship this summer, and the government has also taken tentative steps to broaden language and cultural rights for the large Kurdish minority.

“Turkey is going back to the good side of the Ottoman Empire, said Baskin Oran, an academic who launched a petition apologising for the killings of Armenians in 1915. The Kemalist state, created after the Armenian massacres and population exchange with Greece, assumed non-Turks would be assimilated and non-Muslims expelled. But “if the Armenian taboo is broken, the rest will follow suit,” Mr Oran said.

Boats shuttled about 1,000 worshippers, including visitors from Istanbul, Yerevan, Iran and the US, to Akhtamar on Sunday, where tearful women lit candles and knelt to pray.

“This land has created a lot of Armenian culture. It means a lot,” said Hayk, a 26-year-old from Los Angeles. “It’s a good first step [from Turkey] and I’m hopeful there will be more.”

Paul Shahinian, from New Jersey, said the service was a “bittersweet” reminder of his family roots in Van. “Ethnic hatred runs deep, and it runs through generations. I think Armenians need to have reconciliation and move on . . . but it’s impossible,” he said.

Many diaspora organisations called on Armenians to boycott what they saw as a publicity stunt by a government that denies the 1915 massacres constituted genocide. Ankara says thousands of Turks also died in the empire’s disintegration.

Others cancelled trips at the last moment when the authorities failed to place a cross on the roof.

Minorities living in Turkey still face prejudice – including, in the case of Christian converts, from their own families. The European Court of Human Rights ruled last week that Turkey had failed to protect the Turkish-Armenian journalist Hrant Dink before his murder in 2007. And the government has still not acted on promises to reopen the Greek Orthodox Halki seminary in Istanbul.

But many acknowledge that the AKP, whose religious members also faced pressure in the past from an establishment fearful of radical Islam, has done more to promote tolerance than any previous government.

“Government action is very slow and timid, but it is happening. Comparing it with the Kemalist period is like night and day,” said Cengiz Aktar, an academic at Istanbul’s Bahcesehir university.

Although politicians still tread carefully for fear of reprisals by nationalists, attitudes in Turkey have changed radically in recent years, with new books, films and seminars opening to discussion issues once fixed in stone in the school curriculum.

Moreover, many Turks are becoming aware that their own roots are more mixed than the “Muslim” listed on the identity cards of most would suggest.

“I came to see because my father was one of them,” said Bahar, a local woman in her 70s whose Muslim grandparents adopted a 12-year-old Armenian boy when his family was killed. “I came to see my relations.”

Additional reporting by Funja Guler

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