The Global Fund to Fight Aids, Tuberculosis and Malaria says it will stop funding programmes in Burma, due to increased travel restrictions.
Burma's authorities restrict access to sensitive areas
A spokeswoman for the organisation said that aid workers were unable to carry out their work properly in the country.
It is the first time the Geneva-based organisation has withdrawn from a country in which it is operating.
It said its decision was regrettable, given the serious epidemics threatening the impoverished Burmese population.
Last year the Global Fund agreed to spend $100m over five years combating disease in Burma.
According to UNAids, an estimated 600,000 people in Burma have HIV or Aids, and the country is thought to have one of the highest rates of tuberculosis in the world.
"We have terminated the grants to Myanmar [Burma] as of yesterday," spokeswoman Rosie Vanek told The Associated Press on Friday.
She added that it was the organisation's "basic principle" to ensure that the money it was given was well spent.
"The travel restrictions appear to be the most recent manifestation of a gradual change in the government's attitude towards international and national humanitarian efforts in Myanmar over the past few weeks," the group said in a statement obtained by Reuters news agency.
"The Global Fund has now concluded that the grants cannot be implemented in a way that ensures effective programme implementation."
All the group's activities in Burma are set to cease by 1 December.
The Global Fund - an independent organisation of governments and private groups set up by the UN - works in more than 100 countries, trying to combat deaths from Aids, Tuberculosis and Malaria.
It is not the only organisation to complain of restrictions in Burma.
The head of the UN World Food Programme, James Morris, flew to Rangoon earlier this month to ask the government to let aid workers move more freely to deliver food aid.