Not much happens in Praggi. So when 150 Syrian refugees arrived in the village, high in the flatlands of far-flung north-eastern Greece, it was not something residents were likely to forget.

Some of the Syrians were huddled against the biting cold in the courtyard of the church; others had congregated beneath the trees of a nearby forest. All had made the treacherous journey from Turkey – crossing the fast-flowing waters of the Evros river – in a bid to flee their country's war. Then came the white police vans and the Syrian men, women and children were gone.

"Ever since we have lost all trace of them," said Vasillis Papadopoulos, a lawyer who defends the rights of migrants and refugees. "They just disappeared. Our firm belief is that they were pushed back into Turkey."

Activists, lawyers, human rights groups, opposition MPs, immigration experts and international officials are becoming increasingly concerned about the heavy-handed tactics Greek authorities use to keep immigrants away.

In a recent report released by Amnesty International, Greece was strongly criticised for its "deplorable treatment" of would-be refugees, especially Syrians desperate to escape their nation's descent civil war.

Enforced deportations – highlighted by an alarming rise of migrant deaths – have spurred the criticism.

In contravention of international conventions signed by Athens, coastguard officials and police officers have waged a concerted campaign to stop thousands from accessing EU territory via Greece. Illegal pushbacks have been the focus of those efforts, according to human rights groups.

The drive has intensified as Greece – long seen as the EU's easiest backdoor entrance – has struggled to keep its economic and social fabric together in the face of the country's worst crisis in modern times. Since prime minister Antonis Samaras's conservative-led coalition assumed power in the midst of the crisis last year, authorities have faced charges of violently apprehending migrants, beating them and stripping them of their belongings. Special coastguard units – often masked and dressed in black – have been accused of dumping migrants, without any consideration for their safety, in Turkish territorial waters.

"The number and scale of these alleged incidents raises serious concerns," said Ketty Kehayioylou at the Greek outpost of the UN refugee agency, UNHCR. "We still don't know what happened to the two groups in Praggi," she said. "No one was ever registered at the First Reception Centre as foreseen by national law and we've demanded an investigation."

The claims come as Amnesty International urged Greece to launch an inquiry into comments by the country's police chief, Nikos Papagiannopoulos, in which it is alleged he ordered his officers to make the lives of immigrants unbearable.

"If they told me I could go to a country … and would be detained for three months and then would be free to steal and rob … it would be great," Papagiannopoulos, the highest security official in the land after the public order minister, was quoted as telling officers during a secretly recorded meeting. "We must make their lives unbearable." The comments were published by the investigative magazine, Hot Doc, on 19 December.

John Dalhuisen, Amnesty's director for Europe and Central Asia, said: "If accurate, the deeply shocking statements attributed to the Greek chief of police would expose a wilful disregard for the rights and welfare of refugees and migrants seeking shelter and opportunity in the European Union."

With allegations of torture also on the rise, two senior coastguard officials were jailed last month after a military court found them guilty of subjecting an asylum seeker to a mock execution and water-boarding.

The discovery of ever more bodies – in the Aegean Sea and around the land border Greece shares with Turkey – have also raised the alarm. The German NGO, Pro Asyl, recently estimated that 149 people had died this year – an increase attributed mostly to the enormous risks refugees were prepared to take since Greece sealed its land border with Turkey in August 2012.

Following the construction of the fence – a six-mile barricade topped with thermal and sonar sensors – traffickers have focused on ferrying their human cargo to Greek islands in the Aegean Sea.

"The shift of escape routes has led to the deaths of many people … mostly Syrian and Afghan refugees, among them many children and pregnant women," said Pro Asyl in a report documenting the problems faced by those fleeing persecution and war. (pdf)

"The brutality and extent of violations are shocking," it claimed. "Refugees are being brutally pushed back by Greek authorities. This is happening systematically with the complicity of other European authorities despite the fact that it is against international law."

According to the EU border agency, Frontex, detections of illegal immigrants in the Aegean Sea have increased by 912% since the barbed-wire barrier went up.

"It is a wall of shame, a hair-raising element of Fortress Europe," said Aphrodite Stambouli MP of the radical left main opposition Syriza party. "It is outrageous that people in need of international protection should be obstructed from getting it in this way."

Last week, she travelled to the remote Evros region – passing signs emblazoned with the words "danger: mines" and guards posted at checkpoints – to learn for herself what had happened in Praggi.

"What we know is that 150 Syrians crossed the border because relatives they called, both in Greece and other European capitals, have confirmed that that is what happened," she said.

"They told them clearly, 'We are in a village called Praggi, some of us are in the yard of a church, some of us in a forest.' The police version of events, that only 13 [refugees] were found that day does not add up and that is because they were obviously pushed back over the border."

Immigration experts say blame lies partly with the rise of xenophobia in Greece, where the virulently anti-immigrant, neo-fascist Golden Dawn party is now the country's third biggest political force.

But they add that Greek authorities are under immense EU pressure to do the "dirty work" of buttressing what is widely seen as the bloc's most porous border. "From as far back as 1990, northern Europe's policy has always been that the south has to assume the burden of stopping irregular migration," said Martin Baldwin-Edwards, who heads the Mediterranean Migration Observatory in Athens. "That, growing xenophobia, and the disrespect Turkey and Greece have historically shown for migrants' human rights account for the push-backs."

Last week Turkey signed a deal with the EU promising to repatriate immigrants who illegally enter the 28-nation bloc in return for its citizens being granted visa-free travel across the union.

"It's hugely important," said Baldwin-Edwards. "Turkey is the main point of entry from Asia and the Middle East. The more it is brought into the European ambit and assumes the responsibility of managing Europe's south eastern borders it will lessen the pressure on Greece."

In the forlorn villages of squat one-story homes that dot the frontier's heavily militarised zone, the push-backs have caused consternation even if residents – many hard-bitten nationalists – have welcomed the erection of the wall.

"The fence may have made us feel safer but we also know that all these people want is to pass through," said Nikos Dollis ,who runs a cafe in Nea Vyssa, the last settlement before the frontier in one of Greece's most secretive corners. "Their intention is never to stay here. They want to get out, go to other countries in Europe."

Demonstrators recently protested outside the police headquarters in Orestiada, the gritty town that is the region's biggest metropolis, in a display of outrage over the incident in Praggi. Among them was Natasa Gara, a human rights campaigner who edits Orestiada's weekly newspaper, Methorios.

"We want to know what really happened to the 150 Syrians, whose only crime was to want to escape the war," she said after spending days investigating the affair.

"Are the police saying that everyone in Praggi is mad, that they just thought they saw 150 men, women and children? Because if they are, they are not telling the truth."