All the major buildings, including hospitals, police stations and schools, in the towns were submerged under 4-foot-deep water, Pakistan's GEO TV reported Tuesday.
The abandoned city of Thatta, deep in the Indus River delta, is no longer under threat of being swamped, a spokesman for Sindh province's disaster authority said.
Floodwaters entered Gaji Khuhawar, a town of 40,000, on Monday but most of the residents had already been evacuated, Pakistan's English-language newspaper Dawn reported.
Officials said there was mounting pressure on the town of Warah as floodwaters accumulated in a pocket between two towns near Warah.
A district coordination officer said local residents constructed embankments in Dadu district, impeding the flow of water.
In Makli, some 250 people surrounded the local police station, pelting police vehicles with stones to protest inadequate flood relief efforts.