Ahmad Kamal, a spokesman for the National Disaster Management Authority, said at least 61 people died in the eastern Punjab province since Thursday.
He said another 38 people died in the Pakistan's portion of Kashmir and 11 died in northern Gilgit Baltistan province, AP reported.
Kamal said officials believe all those were killed when the roofs of their homes collapsed.
"We are dispatching tents and other relief items for those who have been affected because of rains and floods," he said. He said the army helicopters and boats were evacuating people from affected areas.
Authorities fear the death toll may rise as more flooding and rain is forecast for the coming days.
State-run Pakistan television showed inundated villages, submerged roads and damaged homes across Pakistan and in Kashmir.
It said authorities briefed Prime Minister Nawaz Sharif on Saturday about the floods.
Pakistan's meteorological service said "widespread rain-thundershowers" were expected Saturday in various parts of the country.
Pakistan, like neighboring India, suffers widespread flooding during the annual monsoon season. In 2010, flash floods killed 1,700 people in Pakistan.