The new warning on Wednesday is for the same southern regions struck by climate-induced catastrophic deluges in 2022 that killed thousands of people.
The National Emergencies Operation Centre said expected rain up to 100 millimetres in the next 24 hours could submerge highways, disrupt transport, and damage power and telecommunications networks in Karachi, Hyderabad, Thatta, Badin, Mirpurkhas, and Sukkur in the southern province of Sindh.
At least 41 people have been killed in rain-related incidents nationwide in the past 24 hours, the disaster management agency said, mostly in the northern Gilgit-Baltistan region and in the city of Karachi, where torrential rains on Tuesday flooded streets and disrupted daily life.
Schools in Karachi remain closed.
Pakistan has suffered above-normal monsoon rains, killing at least 746 people since June 26.
Rescuers in the northwest pressed on with a grim search for nearly 150 people missing in the district of Buner, where floodwaters carrying massive boulders and mud swept through villages, flattening homes and leaving piles of rubble.
Search teams aided by army sniffer dogs pulled more bodies from the debris as anxious relatives looked on.
Prime Minister Shehbaz Sharif and the country's powerful army chief, Field Marshal Asim Munir, visited flood-hit areas in Swat Valley and Buner on Wednesday.
Sharif promised, in a televised speech, financial compensation for the survivors and quick repairs of the damaged infrastructure, while warning residents to avoid building structures near river banks.
Mohammad Suhail, a spokesman for the emergency services, said the death toll in Buner has climbed to 290 after more bodies were recovered.
Rescue teams managed to distribute tents, blankets, cooking utensils, ready-to-eat food, and clean drinking water in the area, he said, as others worked on restoring power in the devastated zone.
Most of the damaged roads have been reopened in Buner.
Survivors recounted horrific stories of sudden floodwaters that carried boulders and barely allowed people to run to safer grounds.
Many residents have blamed the government for not issuing an early warning.
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