Medecins Sans Frontieres (Doctors Without Borders) said in June it had to close two projects, which it said treated around 55,000 mainly Burmese unregistered migrants.
“We had enormous difficulties with the authorities to find strategies acceptable to them and us,” said head of mission in Thailand Denis Penoy.
“We were forced to close one of our private clinics and pushed to close the other,” he added. “We will not conduct any more activities and will have no representation in Thailand.”
Access to healthcare for unregistered migrants at the two medical centres has been central to MSF operations in the country for two years.
But Penoy said the authorities in Samut Sakhon, a port town on the outskirts of Bangkok, instructed the local MSF clinic to limit its work to prevention and told doctors not to treat general practice patients.
Its second surgery, in the Three Pagoda Pass on the border with Myanmar, was also later closed.
Activists estimate there are up to about three million migrants in Thailand, mostly from impoverished neighbour Myanmar, also known as Burma.
More than a million are believed to remain without documents despite a recent government registration scheme.
MSF, which employs around 70 staff in the kingdom, first worked in Thailand in 1975.
Penoy said a return to the country was possible “in the event of an emergency or great need”.