Migrants and asylum-seekers detained in Greece are being forced to endure deplorable conditions, often with devastating effects on their health, according to a report from aid agency Médecins Sans Frontières (MSF).

Doctors who have attended internment camps, police stations and coastguard facilities around the country described "a living hell" for thousands of immigrants denied fresh air, natural light and basic sanitation.

In one detention camp in Komotini, not far from the Turkish border, medics saw human excrement seeping through cracked pipes between the building's floors.

"I did not think that such conditions were possible on European soil," said Marietta Provopoulou, who spent more than a decade working in Africa before returning to Athens to head MSF in Greece. "The main complaint of migrants is that they are not being treated like human beings, that they are being subjected to a living hell," she told the Guardian. "And they are right."

MSF said the practice of rounding up migrants on a massive scale had created a breeding ground for disease in detention centres nationwide.

Outbreaks of scabies in overcrowded camps were commonplace. So, too, were respiratory infections, gastrointestinal disorders, musculoskeletal problems, dental problems. There have even been a few cases of tuberculosis. Unaccompanied minors – mostly from Afghanistan – wrongly registered as adults were also being detained.

"The conditions are shocking," said Panagiotis Tziavas, a MSF doctor.

"Not only are people crammed in a very small area. Another major problem is the sanitary conditions … most of the latrines are in a disgusting state."

Greece is a leading transit point for immigrants desperate to get to Europe from Asia, Africa and the Middle East. Under pressure from the EU to stem the influx, Greece's conservative-dominated coalition began a "clean-up" operation in the summer of 2012, systematically detaining migrants and asylum-seekers, often indiscriminately.

MSF teams with access to detention facilities over the past six years said they had witnessed a surge in the numbers subject to prolonged detention, with most incarcerated for the maximum limit of 18 months. In an atmosphere of far-right anti-immigrant sentiment, there was also the risk of repeated detentions. Even asylum-seekers fleeing war-torn countries such as Syria were being incarcerated for up to 15 months.

"Often migrants are detained for up to 18 months in the holding cells of police stations that were only meant to keep people for a few days," said Ioanna Kotsioni, head of migration policy at MSF Greece.

Many former army camps and military academies were hastily transformed into detention centres overnight. Many fFacilities were cramped and humid with soggy mattresses causing growing numbers to suffer from musculoskeletal problems, the group said.

"Around 6,000 migrants and asylum seekers are currently being detained and the illnesses we are seeing are linked, without doubt, to the squalid living conditions," she added. "In police stations, where bed bugs are common, detainees rarely have access to fresh air, natural light or exercise areas – in violation of European law. In some detention camps they have limited or no access to showers or toilets. And in Komotini, we saw human waste seeping through broken pipes from one floor of the building to the next. The indifference on the part of authorities was extraordinary."

A number of migrants have reportedly tried to take their own lives. One 16-year-old Afghan boy, who had made the perilous journey from his home country to Greece, but was detained in Komotini, recently jumped from the roof of the building in protest over the living conditions, according to MSF.

"We are detained for 18 months. Why? I have come for peace, I am not a criminal," the boy, who broke both his legs, was quoted as telling the relief organisation. "The water of the showers is always cold and the toilets never work. The food is bad, it's not healthy food. Many times I have asked to be released because I am a minor but they have always refused … since they didn't want to release me I thought it was better for me to jump off the roof than to stay here."