Most of the people were killed in Karachi where some areas like Gulistan-e-Jauhar, Amroha Society and Saadi Town are still inundated, they said.
The deaths occurred due to electrocution, roof-collapsing and drowning, said a rescue official of Edhi ambulance service.
National Disaster Management Authorities (NDMA) chairman Zafar Iqbal Qadir said the prevailing monsoon spell has claimed over 69 lives and left 70 injured.
The seasonal rains damaged over 7,000 houses and shops across the country, he said, adding heavy rains may continue for two more days, but rivers are not expected to flood.
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Monsoon also wreaked havoc in Khyber-Pakhtunkhwa in north-west, Balochistan in south-west, interior districts of Sindh and Rajanpur district of Punjab.
Kamran Zia, an other NDMA official, said that eight people were killed in KP and 12 in tribal areas, 10 people in Balochistan and 12 in Punjab.
Hundreds of people have been affected and army was called in Karachi to shift the marooned people to the safe places. Crops over hundreds of hectares have also been damaged.
Officials said the flood situation was under control as most of the river were in either in medium or medium to high floods. In some rivers the water level was already receding.