Thousands of people who fled their homes after floods caused by Koshi river in eastern Nepal are now threatened by epidemics, media reports said Thursday.

More than 40,000 people took shelter in government-run camps, about 5,000 of them were ill and at least two deaths were reported, Kantipur newspaper said.

"People in the camps are increasingly vulnerable to diarrhoea, pneumonia and high fever because of water contamination and lack of proper clothing and sanitation," the newspaper quoted police officers as saying.

"Medical teams are spraying disinfectants in camps as unmanaged garbage is piling up in relief camps," Ramchandra Adhikari of the Nepal Red Cross Society said. "Efforts are being made to send more medical teams to the camps to avert possible epidemic."

It remains unclear how many people were displaced by the flooding, with one estimate putting the figure at more than 50,000.

The government also said it had to deal with tens of thousands of Indian nationals who crossed into Nepal to seek shelter after their homes in the Indian state of Bihar were submerged by flood waters from Koshi.

"About 5,000 Indian nationals entered Nepal on Wednesday seeking help and we estimate the number of Indian nationals now seeking refuge in Nepal to top 20,000," Sunsari chief district officer Durga Bhandari said.

Meanwhile, Nepal's meteorological office said more rains were expected in eastern Nepal likely to cause more floods.

A partial collapse of Koshi's embankment caused last week's floods, inundating dozens of villages. The river is continuing to damage other portions of the embankment threatening more areas.

The Nepalese government said a team of experts started repair work but continuing rains and high water levels were hampering progress.

Despite the scale of the flooding, the number of deaths on Nepal's side of the border has been relatively low. The government confirmed only three deaths with another two dozen people missing.