Tengku Sharifuddin Tengku Ahmad, Najib's press secretary, said the prime minister became  infected with E.coli after criss-crossing the flooded areas last month.
"The prime minister is resting at home," he said in a text message without elaborating.
E.coli are a large and diverse group of bacteria and most strains are harmless.
Rajbans Singh, president of the Malaysian Wellness Society, said the prime minister could have been infected after consuming contaminated food or drinks.
Some kinds of E.coli can cause diarrhoea, he said.
The flooding in the northeast killed 21 people. At its height, almost a quarter of a million people had to abandon their homes.
Najib was forced to return early from holiday in Hawaii after he came under fire when he was filmed playing golf with President Barack Obama last month during the disaster.
Angry flood victims also alleged the government responded slowly, with people in outlying areas stranded without food or drinking water for days.
But following dry weather and as waters recede, many people are returning to clean their mud-filled homes.

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