Martin Panter, the organisation's international president, told the Guardian he had interviewed and examined five reported survivors of the February 15 assault on Karenni positions in Nya My, just over the border from the northern Thai town of Mae Hon Son.
"I believe there's overwhelming and compelling circumstantial evidence that these soldiers are victims of chemical weapons," he said.
"I cannot say exactly what the cocktail of chemicals was but it appears to have contained blister agents, mustard gas and neurological agents." He said the Karenni forces had allegedly been enduring an artillery bombardment for more than a month when, on February 15, a shell exploded with a different sound.
"They said there was a strongly pungent acrid yellow vapour," Dr Panter said. "The gas was yellow, tasted like chilli and was hot."
The Karenni allegedly told Dr Panter their eyes watered, and they suffered severe nausea and vomiting, coughed up blood and suffered gastro-intestinal illnesses such as diarrhoea and had great difficulty walking for some time.
"I have a report from a doctor who examined them five days after the attack and what I saw was completely consistent with what was in that report," he said.
Dr Panter admitted it would be virtually impossible to prove his allegations. "The United Nations insists on date and location-specific photographs and evidence such as shell fragments and soil samples in double-sealed bags," he said. "Many of these chemicals are water-soluble so after the first heavy rain all the evidence would have disappeared."
Burma's military seized power in 1962 and has ruled with an iron fist ever since. The opposition National League for Democracy overwhelmingly won a general election in 1990 but was never allowed to take office.
The junta's senior general, Than Shwe, is currently on a rare overseas visit, to Jakarta, for a summit of Asian and African leaders. No one in his delegation was willing to discuss the allegations last night.