Aid agencies have warned about the heavy toll severe flooding has taken on Bangladesh, saying an estimated 100,000 houses have been destroyed and millions of hectares of crops wiped out.

Key points: About 13,000 cases of diarrhoea reported

About 13,000 cases of diarrhoea reported Worst flooding in country in 100 years

Worst flooding in country in 100 years Bangladesh also dealing with influx of people from Myanmar

The International Federation of the Red Cross said as waters receded the full impact was being realised, with particular concern about the spread of disease.

"There's been a big increase now in watery diarrhoea, that's quite serious, there are about 13,000 cases of that which have been reported," said Tom Bamforth, shelter head, Bangladesh International Federation of Red Cross and Red Crescent societies.

"So there's a significant increase and that's the immediate health issue that we're facing."

With international focus on the plight of thousands of Rohingya refugees fleeing Myanmar for southern Bangladesh, the dire situation in the rest of the country received little attention.

"It's the worst flooding in 100 years. It's even bigger than the floods of 1988 which killed 2,500 people," Mr Bamforth said.

"So the flooding is massive. A third of the country is under water."

Aid agencies say they are concerned about the spread of disease. ( Supplied: Save the Children )

Violence in Myanmar's Rakhine State has led to the exodus of nearly 150,000 Rohingya to neighbouring Bangladesh.

The United Nations World Food Program said it expected that number to double.

Bangladesh said it would not stop them coming, but the already-poor, densely populated country lacks the means to deal with the unfolding calamities.

"You know the longer term outlook is quite bleak, really," Mr Bamforth said.

"I mean the questions remain unanswered about where their next crops are going to come from, in some cases even where their next meal is coming from."

The UN and NGOs have made an urgent appeal for at least $22 million, but so far they have received only a third of that amount.

Save the Children said more than 20 million people in Bangladesh had been affected.