Bulgarian police fired water cannon and rubber bullets at rioting migrants angered at being confined to their refugee camp during a health scare, the interior ministry said.

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The unrest in the camp in Harmanli, a town close to the Turkish border, happened two days after the authorities sealed it off to prevent anyone leaving following local media reports that the migrants were carrying infectious diseases.

Earlier on Thursday, camp residents set fire to furniture and tyres and threw stones at riot police, who deployed water cannon. In the evening, police pushed back a large group trying to leave the camp, which is home to 3,000 people, mostly thought to be Afghans. “We used a water cannon, blanks and rubber bullets as well as physical force,” said Georgi Kostov, the interior ministry’s chief secretary, outside Bulgaria’s biggest refugee camp.

“Over 40 of the most rampaging migrants were detained. They will be charged,” he said, adding that four police officers had been wounded. He said was not aware of any wounded migrants.

Reflecting the gravity of the situation – and the political impact of the migrant crisis – the prime minister, Boiko Borisov, was on his way to the camp late on Thursday, a spokeswoman said.

Harmanli townspeople staged a protest last week calling for the camp’s closure after media alleged that migrants there carried communicable skin diseases. The head of the Bulgarian refugee agency, which runs the camp and took the decision to seal it temporarily to allow health authorities to investigate, told Bulgarian national radio that those reports were false.

Bulgaria has built a fence on its border with Turkey and has bolstered its border controls to prevent migrants entering. Around 17,000 were detained in the first 10 months of the year, down by more than a third on last year.

Despite the decreasing numbers of arrivals, Bulgarian nationalists have staged protests in recent months calling for the immediate closure of all refugee centres and for migrants to be returned to Turkey or their countries of origin. They say Bulgaria, the EU’s poorest member state, cannot afford to support them in such numbers.