Health officers administering the polio vaccine in the 11 counties might fail to meet their target.
This follows the heavy rains and floods that have rocked most parts of the country.
Nairobi County Health Representative Lilian Mutua says most officers have been forced to halt the exercise following the heavy downpour.
Mutua says that some have even been hindered from getting to their destinations by floods that have occurred in several parts of the country.
The exercise is currently going on in 11 counties, Nairobi, Mombasa and Marsabit counties included.