A freezing and squalid Belgrade railway depot where up to 2,000 people are seeking shelter from the bitter Serbian winter risks becoming a “new Calais” for refugees and migrants abandoned by European authorities, the humanitarian group Médecins Sans Frontières has warned.

Children as young as eight are struggling to survive temperatures that have plunged to -16C this week, with no running water or sanitation.

At a Belgrade clinic set up by the charity, doctors have seen frostbite and burns resulting from the inhalation of toxic smoke, as people burn anything they can find to stay warm, among dozens of other medical problems.

MSF estimates that up to 2,000 people are living in a cluster of warehouses and other buildings around the city’s main station. It estimates that nearly half the patients they have treated are under 18.

“Serbia risks becoming a dumping zone, a new Calais where people are stranded and stuck,” warned Andrea Contenta, humanitarian affairs officer for MSF in Serbia.

The country is not part of the European Union, but it borders several countries that are part of the bloc, including Hungary, Bulgaria and Romania, and has become a key transit point for those hoping to start a new life in western Europe.

Serbia won praise for its treatment of migrants, but increasing numbers have become stranded there as the EU tried to shut down the Balkan route and tightened border controls. Processing camps are now badly overcrowded and more people are arriving every day. Although they ultimately hope to move on from Serbia, many are spending months there, making repeated failed attempts to cross into the EU.

“We cannot continue avoiding talking about reality, which is that the Balkan route is still open but people are getting stuck because there is no safe way to travel,” Contenta said. He added that unofficial estimates were that up to 8,000 refugees and migrants were stranded in Serbia.

A person collects water outside a crumbling warehouse that has served as a makeshift shelter in Belgrade, Serbia. Photograph: Darko Vojinovic/AP

The grim conditions endured by thousands outside the government camps were highlighted at the start of this week when a freezing cold snap put lives at risk. MSF was given permission to try to heat the derelict shelters, where there is no glass and walls and roofs are full of holes.

“It was –16C outside and we managed to get the warehouse to –1C,” said MSF spokeswoman Gemma Gillie. There is also no sanitation and an application to set up toilets and showers, submitted to Serbian authorities a month ago, has still not been approved.

The cold has already claimed too many lives. Writing in the Observer, William Lacy Swing, the head of the UN’s International Organisation for Migration (IOM), said the plight of migrants and refugees should be a focus for leaders gathering in Davos for the World Economic Forum this weekend. “They should reflect on the growing number of helpless migrants who have frozen to death in the current cold snap, with the possibility of many more to be found in a grim archipelago of makeshift settlements,” he wrote.

The warehouses used as temporary shelter in Serbia lie behind the main Belgrade train station in a litter-strewn no-man’s land dotted with puddles and wintry sludge. Graffiti is scrawled across many of the walls.

“No one leaves home unless home is the mouth of a shark,” reads one message on the wall of the former Railwaymen’s Club. Other messages read: “We are helpless” and “Please don’t forget about us.”

The air is thick with the smoke of a dozen fires of railway sleepers smeared with tar and other toxic, scavenged fuel; some smoke billows out of broken window panes. “We sleep here,” said a small child, who gave his age as eight, as he guided a visitor around the large warehouse.

Some refugees have set up small tents inside the building alongside empty cans, plastic bottles and waste, while other groups have used sheets of plywood, empty bookcases or doors to block off their own areas of muddy floor space.

People wash themselves outside a makeshift shelter. Many people are stranded in Serbia as they try to make their way to Europe. Photograph: Darko Vojinovic/AP

“There’s no place for sleeping, no good food, nowhere to have a shower. There are so many sick people, there’s no medicine,” says Shamir Khan, a 22-year-old Pakistani from Sadda on the Afghan border, who says he worked in human rights before fleeing the country.

Peter Van der Auweraert, western Balkans coordinator for the IOM, said the Serbian government had offered places in reception centres for everyone living in the warehouses, but were turned down. Although conditions were not ideal in some centres, he said they ensured that people had basic protection from the cold. He feared migrants were being exploited for cash and politics.

“These people are refusing to move for a couple of reasons. Based on the stories that migrants tell us, it seems that some smugglers have infiltrated the groups and threaten them – [saying] ‘If you go to these centres, you will not be able to get to Europe’,” he said.

“Some of the more radical activists are doing the same thing, saying, ‘You should stay and tell Europe how you are suffering here.’ To my mind these people are being used to make a political point.”

The refugees gave several reasons for not going to the official camps, saying they were closed or only took families, but most of all that they feared deportation to Bulgaria or Macedonia. “We had so many problems in Bulgaria, so many problems with the police and the people. There is a mafia and people were kidnapped,” says Khan.

When the UN warned this week that European countries were mistreating refugees in cold weather, three of the five deaths it cited were in Bulgaria. The country has become notorious among refugee and human rights groups for its mistreatment of migrants, who arrive across a land border with Turkey or are deported back from other EU countries under the Dublin agreement. That provision means asylum seekers coming to the bloc must stay in the country where they first arrive.

“Bulgaria has been registering them since the very beginning, which means that their first country of entry is Bulgaria. Even if they go somewhere else, they could be legally brought back,” said Daniel Smilov, programme director at the Centre for Liberal Strategies, a Sofia-based thinktank.

Both official security forces and vigilante groups have been accused of brutality. People trying to cross the country are often wary of seeking help or shelter, making them particularly vulnerable.