Officials said on Saturday thousands of people were suffering from diarrhoea.
Nearly 7000 cases of water-borne diseases had been reported since Friday alone, while the official toll from the floods rose to 489, the officials told the official BSS news agency.
Although river levels were falling, water was receding at a slow rate.
Floodwaters have inundated 40 of the country's 64 districts, including two-thirds of the capital Dhaka, and affected some 30 million people. Officials have put the cost of the damage to property and infrastructure at $6.6 billion.
The flooding is the heaviest since 1998 when the country's worst floods claimed the lives of more than 700 people.
The government is working with international aid agencies to distribute emergency relief and coordinate post-flood rehabilitation programmes.
The World Food Programme, which is distributing rice and water-purification tablets to flood victims, has warned that Bangladesh "could face a major humanitarian crisis" in the coming days.