Flood waters have risen dramatically after several days of heavy rain in Karen State forcing thousands to flee to nearly 80 relief camps, Chum Hre, director of the social welfare, relief and resettlement department told AFP.
"Altogether 24,499 flood victims have been evacuated" in Karen State, he said, adding hundreds more had been displaced in Mon and Rakhine states.
"It is very difficult to reach some of the disaster-hit places because of the bad weather and landslides," he said, adding that helicopters had been deployed.
Heavy rains also inundated areas across the border in Thailand.
Seven Thai provinces remained flooded on Wednesday, the Interior Ministry said in its daily update.
Three people have died since Monday after they were hit by trees felled by fast-moving water, it added.
In Thailand's western town of Mae Sot, which borders the flood-hit area of Myanmar, waters have receded in the town centre but remain high in outlying areas, especially near the frontier checkpoint.
"The situation has returned to normal in Mae Sot city," Pramote Chantasri, of Mae Sot City Municipality told AFP.
"The worst was on Monday after four days of heavy rain in the mountains," he said, adding the bridge between the two countries remains open.
Parts of Thailand and Myanmar are inundated each year during the monsoon period, which ends in October.
Deadly floods in 2011 left more than 800 dead in Thailand, inundating swathes of the country for months, deluging parts of the capital and taking a heavy toll on the country's lucrative manufacturing industry.