"People are evacuating in a hurry, complaining that they have not received any help from the government," he said.
At least 47 people had been killed in Punjab, Pakistan's National Disaster Management Authority said.
Nearly 1,000 villages have been affected and some 15,000 houses destroyed in the province, according to the UN.
The rush of muddy water over river banks in Punjab threatened to destroy vast stretches of crops that make the province Pakistan's breadbasket.
The army used boats and helicopters to move stranded villagers in the area to higher ground.
Water levels were so high in large tracts of Kot Addu and the nearby area of Layyah in the south of the province, that only tree tops and uppermost floors of some buildings were visible.
A military spokesman told reporters that at least 30,000 people have been rescued from flood-hit zones in Kot Addu and nearby areas over the previous 72 hours.
He warned that more flooding was expected as weather forecasts predicted more rains in the next few days.
"People must co-operate with us, and they must leave those areas where floods are going to hit," he said.
This year's monsoon season has prompted the worst flooding in Pakistan in living memory.
The northwestern region of the country was the worst hit, until flood waters flowed downstream to inundate large areas in the south.
The UN is scrambling to provide food and other assistance to millions of people affected in the water-soaked nation, which was already struggling with violence and a poor economy.
|The worst affected areas are in red; moderately affected areas are in yellow. Evacuations are underway in the stripped area of Southern Sindh province
It has warned of serious food shortages following the loss of farm produce in the floods. The World Food Programme has estimated that 1.8 million people will need to be fed over the next month.
"People [in the flood areas] are literal fighting to get food aid”, Al Jazeera’s Imran Khan, reporting from the capital, Islamabad, said.
Rescue workers have struggled to deliver aid because of washed-out bridges and roads and downed communication lines.
Several foreign countries have stepped in to help, including the United States, which announced on Tuesday that it was sending six large military helicopters from Afghanistan to help with the relief effort.
But many flood victims have complained that aid is not reaching them fast enough or at all.