Agency epidemiologist Anders Tegnell told TT that 195 cases of the disease have been reported this year.
He said that children may be infected by adults who do not know they are carrying the disease.
In a statement on its website, the agency said that infants who are not old enough to be vaccinated against the disease are at the greatest risk.
The agency added it is researching the best ways to combat the disease.
Whooping cough is caused by bacteria and is normally treated with antibiotics.