On the outskirts of Simferopol a cluster of uneven houses and a mosque cling to the edge of the highway. "This was once just a field, but now we have built our own city. We built this with only our bare hands and a few tools," says Dzhalil Ibrahimov, a member of the Mejlis, the Tatar council which represents Crimea's Muslim minority. "This is a creation of the Tatar people. The state didn't help us as at all."

The Tatars' existence in Ukraine has long been precarious. In 1944 Stalin ordered that the Sunni Muslim group be deported en masse on the pretext that they had collaborated with the Nazis. Crammed into cattle-wagons, nearly half of them died before they had even reached their destination in the wastelands of central Asia.

"We have all grown up with these terrible stories from our grandparents," says Timer, a 20-year-old construction worker who lives in the village of Pionerskoe, known in Tatar as Eskisarai. "The history of the Tatar people is filled with hardship."

After the fall of the iron curtain in 1989 the Tatars flocked back to their ancestral homelands in Crimea – only to find their old houses occupied by Russian families.

They now make up around 12% of the peninsula's population, but battles over property rights as well as differences in culture and religion have limited the group's reintegration with the region's ethnic Russian majority.

A Crimean nationalist group called Russia Unity has openly organised attacks on Tatar properties and desecrated graveyards. Last week, the leader of the party, Sergei Aksyonov, was named Crimean prime minister after Russian forces seized control of the peninsula.

Graffiti in Simferopol reads: 'The Russians are coming - resistance.' Photograph: Vadim Ghirda/AP

Now, as Crimea faces a referendum that is likely to seal its fate as a province or satellite of Russia, ethnic tensions are reaching boiling point. In a chilling echo of history, Tatar houses in the Crimean city of Bakhchisarai have been marked with an ominous X, just as they were before the Soviet-era deportations. On Monday two Tatar businesses were firebombed.

"This referendum is a humiliation. What is a choice while staring down the barrel of a gun?" asks Refat Chubarov, chairman of the Simferopol-based Mejlis. The Tatar leader has called on his people to boycott Sunday's vote. "[It] is an illusion, a cheat. The results are already decided," he says.

The prospect of a return to living under Moscow's rule is disturbing. "People are in panic. Our nation survived a genocide and there is a fear that there will be a repeat of '44," says Delyaver Akie, secretary of the Mejlis. On Akie's desk the European Union and Tatar flag hang side by side. "We are trying to keep people calm but they are scared of the Russian soldiers and Cossacks that come here," he said. "We just want peace, freedom, and the rights for which we have fought for 20 years. It seems we are about to lose all of this in a blink of an eye."

This time, however, the Tatars are adamant they will not go anywhere. "We came back to our motherland and we will not leave again. We will die here, one way or the other," says Ibrahimov. Amid fears of attack from the increasingly aggressive pro-Russian militia who patrol the streets, Tatar community leaders have organised self-defence units to patrol their villages. "We guard the exit and entrances. We men stay awake all night so that our grandmothers, mothers and children can sleep safely," says Ibrahimov, who commands a unit of 30 men.

Tatar men pray at a mosque in Bakhchisarai. Photograph: Thomas Peter/Reuters

Since their return to Ukraine the Tatars have been a prominent force in the country's political struggles, and Tatar activists were on the frontlines of the 2004 Orange Revolution and the recent protests in Kiev that ousted Viktor Yanukovych's corrupt regime. But with Russian troops camped out in their backyards, their position in Crimea looks weaker than ever.

"There is a feeling that the Russians are waiting for any provocation. The atmosphere is very tense. We don't want to provoke at all," says Ibrahim Abdulov, a pensioner.

The Crimean Tatar TV channel ATR is also under attack. "We are expecting every second to be closed down," says Ayder Muradosilov, the station's creative producer. For more than a week his staff have been camping out in the office 24 hours a day in an effort to keep the only remaining independent channel in the region on air.

Other local TV stations considered to be anti-Kremlin have been mysteriously replaced with pro-Russian channels. ATR's journalists have been beaten in the street and the station's servers, which transmit its online service, are under almost constant attack by hackers.

Women hold a demonstration calling for peace in Bakhchisarai. Photograph: Spencer Platt/Getty Images

"This is a situation which makes us cry. It is almost certain we will be shut down in a matter of days," says Muradosilov.

The depth of the crisis – and the near certainty that Crimea will vote to secede from Ukraine in Sunday's referendum – have sparked rumours that some Tatar leaders are seeking to negotiate surrender terms with Moscow. Senior Tatar figures have reportedly been offered lavish funding, senior positions in a new Crimean government and guarantees of Tatar cultural and language rights.

Chubarov, the Mejlis chairman, has denied those reports. "How could I talk about such opportunities, such negotiations, when my people are in danger?" he says.

But speculation of a pact with Moscow has grown following reports this week of a telephone conversation between the Russian president, Vladimir Putin, and Mustafa Dzhamilev, a prominent Tatar leader and a deputy in the Ukrainian parliament since 1998. According to Russian media the one-hour phone call resulted in both parties stating that they were open to continuing negotiations when necessary.

At the side of the road to Pionerskoe, a group of several hundred Tatar women and children gathered earlier this week to protest against the Russian occupation.

Clutching a homemade banner reading "no war" was Rimma Morozova, a retired woman who returned with her family to Crimea in 1993 after nearly 50 years in exile in Uzbekistan.

"The scariest thing is that our men are not armed. Our people bear a great weight on their shoulder of our people in these times. There is a real fear of war," she says. "We are hoping against hope that everything will be all right, but the evidence says otherwise."

A few cars honked at the demonstrators in a gesture of solidarity, but most drivers sped on past without a second glance.