He said the storm's intensity was decelerating and would subside by evening.
Most of the 120,000 residents of the southwestern port city of Gwadar were moved to higher ground, Abdul Ghaffar Hoth, the city's mayor, said. People from other smaller towns have also moved inland to escape the cyclone.
"We have imposed an emergency in the district and asked the army and other forces to be on alert," he said.
Communication links cut
Residents said the latest cyclone had severed road and telephone links to the affected coastal region.
At least three small boats were reported to have sunk and 18 fishing boats were missing as the navy sent a warship and two helicopters to search the seas for vessels caught up in the storm.
Chaudhry said that the "worst appears to be over" for southern Sindh province, which was battered by the storm at the weekend, but that widespread rains would continue until late on Tuesday.
The clean-up is under way in Karachi, the capital of the province, but many areas remain without electricity or drinking water and several riots have broken out over the situation.
Kamal Hyder, Al Jazeera's correspondent in Karachi, said: "The water resources of the city are badly contaminated, electric poles are down, telecommunications are down.
"The biggest concern now is that epidemics may follow if the clean-up is not done properly."