The doctor, identified as Ishaq Kakar, was shot dead by the gunmen near Sohrab Goth area of Karachi yesterday, officials said.
Prime Minister Raja Pervez Ashraf strongly condemned the killing of the doctor, saying his killers were the enemies of religion, the country and humanity.
He said their barbarism is evident from the fact that they did not have any regard for the Islamic holy month of Ramzan that began today.
Ashraf directed the Sindh government to ensure the safety of people working to help the poorest of the poor.
On July 17, two staff of the WHO, including a Ghanaian national, were injured when unidentified gunmen fired at a UN vehicle near a polio vaccination camp in Sohrab Goth area.
The attacks came in the wake of threats from the Taliban against a campaign to immunise 34 million children against polio.