The group, known by its French acronym MSF, said in a statement Friday that it is "deeply shocked" by Burma's decision to stop its activities after more than two decades of work. It said the move would have a "devastating effect" on its patients.
The aid group is the largest provider of HIV drugs in Burma, supplying treatment to 30,000 people.
Burmese authorities say the order to halt operations only applies to western Rakhine state, home to Muslim minorities including the stateless Rohingya.
In an interview with VOA's Burmese service, a government spokesman said the group has been asked to cease operations until it can negotiate an agreement with the Burmese government.
“The Memorandum of Understanding [MoU] between Burmese government and MSF has been expired since January 2013. We are in the process of signing new MoU. Until we sign the new MoU, the Rakhine government asked MSF to stop its operation in the state.”
Earlier, he criticized the group's public comments that more than 40 Rohingya were killed in an attack in the remote northern part of the state last month. The government insists that only one Buddhist policeman died.
The United States said Friday it was very concerned about the situation. A State Department spokeswoman Jen Psaki urged Burma's government to ensure "unfettered access" for humanitarian agencies.
Burma's government refuses to officially recognize the Rohingya Muslim minority. It says members of any officially recognized minority must be able to prove their ancestors lived in Burma before the British invaded Rakhine in 1823.
Many of Burma's hundreds of thousands of Rohingya Muslims say their ancestors have lived in Burma for generations; but, the impoverished minority group lacks the documentation to prove it.
This report was produced in collaboration with the VOA Burmese service.