The non-profit Edhi Foundation said scores may have been killed by the sweltering weather, with double the usual number of bodies sent to the city's morgues in recent days.
"We have received 180 dead bodies in the last four days which is more than double of what we receive normally," said Faisal Edhi, head of the welfare organisation which oversees a variety of public health projects -- including morgues and ambulance services.
"The majority of these were sudden deaths because of the heatwave as claimed by their relatives, which we cannot independently verify."
The provincial government in Sindh province disputed the estimate.
"Only one casualty has been reported due to heat stroke so far," said Muhammad Ali Shaikh, Director of the Provincial Disaster Management Authority in Sindh told AFP
The heatwave coincides with the beginning of Ramadan, when millions of devout Pakistanis abstain from food and drink from sunrise to sunset.
The Pakistan Meteorological Department warned "hot to very hot weather is likely to prevail in Karachi during next 2-3 days", forecasting highs of 44 degrees Celsius during the period.
Aamir Habib, from Karachi's Korangi, said his brother was among the dead and had been rushed to the hospital after collapsing at work on Monday.
"The doctors said he died because of heat stroke," Habib told AFP.
The mega port city, capital of southern Sindh province, is hit by frequent power cuts and has few green spaces.
People living on its crowded streets have little access to shelter or safe drinking water, making them acutely at risk in blistering temperatures.
In June 2015 about 1,200 people died in southern Pakistan during a heatwave, with nearly two-thirds of the victims homeless people.
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