The BBC reports that at least 10 people in the southern metropolis have been killed by the Naegleria fowleri amoeba, which is found in warm bodies of fresh water such as lakes, ponds, and rivers.
It is thought that there may also have been other cases that have gone undetected.
The virulent microorganism usually invades the central nervous system via the nose, from where it makes its way to the brain, which it proceeds to consume piecemeal using a special sucking apparatus.
Besides a stiff neck as well as changes in taste and smell, telltale symptoms also include fever, nausea, and vomiting
It is estimated that 98 percent of infections end up being fatal, with the patient dying 7-14 days after exposure.
Although people are usually infected by swimming in contaminated water only one of the Karachi victims had been bathing.
It is thought that the remainder may have picked up the amoeba while washing out their nostrils as part of the wudu cleansing ritual practiced by many Muslims.
In an attempt to reduce the risk of infection, the Karachi authorities have increased the amount of chlorine in municipal water supplies.
A public-awareness campaign has been launched and people have been urged to use boiled or chlorinated water to wash their nostrils.
Health workers in other cities across the region have also been put on high alert.
WATCH: The deadly Naegleria fowleri brain-eating amoeba