The international medical organisation Médecins Sans Frontières said it has been forced to end its operations in Thailand following interference from the government over its treatment of undocumented migrant workers.

Medical professionals fear many thousands of migrant workers could be unable to get regular medical care after the organisation ends more than 30 years of operations in the country.

"We had enormous difficulties with the authorities to find strategies acceptable to them and us," the organisation's head of mission in Thailand, Denis Penoy, told the Agence France-Presse. "We were forced to close one of our private clinics and pushed to close the other. We will not conduct any more activities and will have no representation in Thailand."

An official with the organisation, based in Brussels, confirmed that, while the Thai authorities were happy for MSF to work on health education and disease prevention, they were not happy with it carrying out primary care. The organisation said this care was vital for thousands of vulnerable migrant workers who have no alternative means of care.

The organisation's problems first became public this summer when it was forced to shut down two clinics where it treated up to 55,000 migrants, the majority of them Burmese refugees who have poured into the country in recent decades. Providing healthcare to migrants at these clinics, one at Samut Sakhon, on the outskirts of Bangkok, and at Three Pagoda Pass near the Thai-Burmese border, had become the main focus of MSF's work in Thailand in the last couple of years.

Officials have indicated that no other organisation is going to take on the role from MSF, which has worked in Thailand since 1975 and currently employs around 70 people in the country.

There are anywhere up to three million migrants in Thailand, and as the situation in Burma has worsened, especially in the east of the country where Karen rebels have increasingly come under attack by the Burmese army, more arrive. Along the border is a string of camps that house approximately 140,000 refugees.

Over the years, Thailand has tried to walk a careful line regarding these migrants, assisting those international organisations that operate the camps while at the same time trying not to encourage more people to make the journey across the border. Earlier this year, the then head of the national security council threatened to close the camps and force the occupants to return to Burma, using the excuse of the election in 2010 of a supposedly civilian government. Following Thailand's own election this summer of Yingluck Shinawatra, the country's first female Prime Minister, a review of this policy was due to be carried out.

The Thai authorities have been working on a plan to register migrant workers through a nationality verification process in which they become legal and are entitled to health benefits through social security. Under the scheme, they have to contribute around 5 per cent of their salary to the fund. It is believed that fewer than 500,000 workers have so far registered. Those who do not register are not eligible for health treatment. The Thai authorities have yet to comment on MSF's announcement.