The move could leave thousands of migrants in the country without access to a doctor.
The group said in June it was forced to close two clinics that treated around 55,000 people, most of them unregistered Burmese migrants.
Providing healthcare to unregistered migrants has been central to the aid group's operations in Thailand for the past two years.
They said authorities in the port town Samut Sakhon, on the outskirts of Bangkok told the charity's local clinic not to treat general practice patients and limit its work to prevention.
The group has not ruled out a return to Thailand in the event of an emergency.