Musa Khan, in charge of WHO's Disease Early Warning System in Pakistan, said on Tuesday that the deaths were reported from March to September.
He says municipal authorities have launched a campaign in Karachi to ensure the supply of clean water to residents.
Symptoms caused by the amoeba include fever, nausea, vomiting, stiff neck and headaches.
The amoeba — Naegleria fowleri — lives in warm, unclean water. It can infect the human nervous system, though this occurs rarely.
Khan says those cases are difficult to treat, and victims can die in five to seven days.