Hundreds of families have been displaced by flooding in the city of Mombasa along the Kenyan coast after days of heavy rain, a humanitarian official has said.

"One hundred and thirty families [an average family has six members] have been affected by the flash floods," Anthony Mwangi, the public relations manager of the Kenya Red Cross Society (KRCS) said on Tuesday.

At least two children were killed when the roof of the house they were sleeping in collapsed due to the heavy rain, he said. Another person was injured.

Most of the displaced are living with relatives and friends, he said, after their houses were destroyed. The roofs of at least 34 houses were blown off in the Jomvu and Bomani areas of Likoni.

Moreover, there is a threat of waterborne diseases as heavy rains continue, raising water levels substantially in other areas of the city such as Bombolulu and Mishomoroni, he said.

Some latrines have collapsed due to the rains and there is a need to ensure the people have access to safe drinking water, he said.

"Mombasa has just come out of a cholera outbreak; we are trying to ensure that the health of the people is safeguarded," he said.

So far, the Red Cross is providing the affected families with non-food items, comprising tarpaulins, kitchen sets, blankets and soap, he said.

Meanwhile, he said, KRCS volunteers were carrying out an assessment on the ground to ascertain the full extent of the damage caused by the flooding.