The poison of sectarian hatred is spreading to Turkey from Syria as a result of the Turkish government giving full support to militant Sunni Muslims in the Syrian civil war.

The Alevi, a long-persecuted Shia sect to which 10-20 million Turks belong, say they feel menaced by the government’s pro-Sunni stance in the Shia-Sunni struggle that is taking place across the Muslim world.

Nevzat Altun, an Alevi leader in the Gazi quarter in Istanbul, says: “People here are scared that if those who support sharia come to power in Syria, the same thing could happen in Turkey.” He says that the Alevi of Turkey feel sympathy for the Syrian Alawites, both communities holding similar, though distinct, Shia beliefs and the Alevi oppose Turkey’s support for rebels fighting to overthrow Syria’s Alawite-dominated government.

Download the new Independent Premium app Sharing the full story, not just the headlines

Sectarian faultlines between the Sunni majority and the Alevi, Turkey’s largest religious minority, have always existed but are becoming deeper, more embittered and openly expressed. Atilla Yeshilada, a political and economic commentator, says that “anything [Turkish Prime Minister Recep Tayyip] Erdogan says against the Alawites of Syria is full of sectarian innuendoes for the Alevi”.

Alawites who have fled to Turkey to escape the violence in Syria often find they are little safer after they have crossed the Turkish border. They say they dare not enter government-organised refugee camps because they are frightened of being attacked by the rebel Free Syrian Army as soon as it is discovered they are not Sunni.

Some Alawites have found their way to Istanbul where they are being looked after by the Alevi community. “A month ago we found Alawites wandering the streets of Istanbul and sleeping in parks where they earned a little money selling water and paper bags,” says Zaynal Odabashi, the head of the Pir Sultan Abdal Alevi cultural and religious centre in Gazi district where 180,000 out of a population of 520,000 are Alevi. He says that “we decided to take them in though the governor of Istanbul told us not to”, explaining that some 40 Syrian Alawite refugees are living in large tents at his centre alone and another 400 have been found places to sleep in houses nearby. The three million Syrian Arab Alawites may differ in religious practices from the Turkish Alevi, but they both follow core Shia beliefs such as reverence for the Twelve Imams. They both feel threatened by Sunni militants and know they are easily identifiable as even the poorest house has pictures of the Shia saints on the walls.

“They consider us as non-believers,” says Mr Odabashi, adding: “Of course, our people feel sympathy for the Alawites and we are against Turkey’s involvement in the war in Syria.”

Alawite refugees fed and housed by the Alevi tell grim tales of torture, disappearances and death. On a mat outside a big tent at the Pir Sultan centre lay an elderly looking man who said he is a Turkoman Alawite from Damascus whose district had been captured by the Free Syrian Army that held him and his 12-year-old daughter for up to 27 days.

His frightened eyes darted nervously around as he said his name was Ali Jabar and he was not sure of some details of what had happened to him because he had been blindfolded all the time he was held. His captivity began when there was a ring at his door at midnight and a voice said a neighbour needed to see him, but when he opened the door a man hit him on the head with his gun butt.

He was blindfolded by his captors whom he identified as the Free Syrian Army. They asked him if he believed in Bashar al-Assad and demanded he curse Imam Ali, but he had said: “No, not even if you cut my throat.”

Daily coronavirus briefing No hype, just the advice and analysis you need Enter your email address Continue Continue Please enter an email address Email address is invalid Fill out this field Email address is invalid Email already exists. Log in to update your newsletter preferences Register with your social account or click here to log in I would like to receive morning headlines Monday - Friday plus breaking news alerts by email Update newsletter preferences

They whipped him and set fire to a plastic bag so molten plastic dripped on to to his back. He rolled up his shirt to reveal half-healed whip marks and burns and took off his shoes to show where several of his toenails had been ripped out with pliers. He expected to be killed, but instead the men who held him threw him out of a car on a country road where he was found by a shepherd. He does not know what has happened to his daughter.

Ali Jabar later met other Alawite Turkomans who had fled from Aleppo and were sleeping in parks in Damascus. They managed to secure enough money to take 42 of them to Turkey in a bus, but they thought it was too dangerous for them to enter Turkish refugee camps. They finally reached Istanbul where they did not know where to go until the Alevi of Gazi offered to help them. Turkish government supporters deny or play down the connection between the Alevi and the Alawites but there is a common bond as both feel endangered by growing Sunni hostility to all Shia sects, regardless of their precise religious beliefs. Dogan Bermek, the president of the Alevi Foundation, a lobbying group mostly made up of better-off Alevi, asserts: “In Syria and in Turkey we are all the same Alevi. The differences between us are only regional because we have developed in different regions without contacts. We are on the same road though it has a thousand paths.”

How great is the danger of Sunni-Shia hostilities that have torn apart Iraq, Syria and Bahrain in the last decade erupting in Turkey? There are marked differences in religious observances between the Sunni majority and the Alevi who do not use mosques, but worship in some 3,000 prayer houses where men and women dance and sing during services. As a large Shia minority under the Ottoman Empire, the Alevi were persecuted and massacred as dissidents and potential sympathisers with the rival Shia Safavid empire in Iran. Oppression of the Alevi was much like that of Roman Catholics in Ireland by Britain from the 16th century on and it continued after the foundation of the modern Turkish state, with at least 8,000 Alevi Kurds of Dersim in the south-east being slaughtered in the late 1930s.

The Alevis became the bedrock of opposition movements in Turkey and make up much of the membership of leftist parties. In 1993 their spiritual leaders, intellectuals and artists held a festival in the eastern city of Sivas to celebrate a 15th-century poet. Trapped in a hotel by a mob of thousands of Sunnis protesting, among other things, at the presence of the Turkish translator of Salman Rushdie, some 35 people were burned to death without the police intervening.

Three years later there was an assault on Alevis by the police, killing 20 people in the same Gazi quarter where Syrian Alawites are now taking refuge.

Since Erdogan won his first general election in 2002 there has been less state violence. But during the protests that started in Gezi Park in Istanbul this summer, all five of the demonstrators killed across the country came from the Alevi community.

This is probably as much a token of their prominence in protests as it is of the police targeting them. It is also a sign that Alevi anger is growing because of memories of past violence against them; discrimination which turned them into second-class citizens and lack of state recognition or support for their religion.

I attended a meeting in an Alevi prayer house called a Cem in Umraniye district on the Asian side of Istanbul, where Alevi activists were setting up an organisation to fight for their rights. Complaints about discrimination abounded: an attempt to set up a joint Sunni mosque and Alevi prayer hall in Ankara was condemned as an attempt to assimilate them and as unworkable because the Alevi would be singing when the Sunni were praying. A delegate said Alevi did not fast at Ramadan but at another time of year, making cohabitation in the same building difficult. There was a lack of state education about Alevi beliefs and resentment at Sunni slanders about their religion.

“The government doesn’t treat us as human beings,” said one delegate. “We pay taxes but we don’t get anything back.”

Resentful though the Alevi are at their treatment, they are at least dealing with a powerful government capable of meeting many of their demands. Mr Erdogan has no difficulty in apologising for events like the Dersim massacres carried out on behalf of a secular authoritarian state in the past. The Alevi do not forget past persecution, objecting to the government’s intention to name the third Bosphorus bridge after Selim the Grim, an Ottoman Sultan of the early 16th century regarded as an ogre by the Alevi, whom he slaughtered by the thousand. Not all the reasons are negative for the greater Alevi sense of identity and willingness to be more vocal in demanding their rights: Turkish security forces under Mr Erdogan are less violent than they used to be and protesters are less likely to be imprisoned or harassed by the state.

But the Sunni-Shia civil wars exploding in Syria and Iraq are deepening sectarian differences among the 1.6 billion Muslims in the world.

Turkey is no exception to this trend, has a large Shia minority and is close to the heart of the turmoil. There is already talk of the “Pakistanisation” of Turkish provinces like Hatay and Mardin, which are used by al-Qa’ida-linked groups fighting in Syria as their rear bases. Turkey’s open border policy for rebels means that the Syrian war is spilling across the frontier.

Successful though Turkey has been politically and economically in the past decade, the long battle for power between the AK party and an authoritarian, secular state has created lasting divisions in society. The rising political temperature in Turkey and the region makes rising sectarian differences ever more explosive.