Pakistani flood survivors migrate to safer areas in the historic city of Baseera near Multan, Pakistan, on Monday. (Khalid Tanveer/Associated Press)

Flood waters that have devastated Pakistan for five weeks headed to the Arabian Sea on Tuesday after swallowing two final towns, but the challenges of delivering emergency aid to some eight million people remained.

The floods have moved down from the mountainous northwest, submerging or affecting large swaths of the country at their peak.

Waters have begun to recede in the north and in Punjab, but they have been submerging towns in southern Sindh province close to the Indus River over the last 10 days.

Government official Hadi Bakhsh said the last two towns in the path of the floods were hit late Monday.

"The flood waters hit Khahre Jamali and Jati towns last night, and now there is no other village or town in the way of the deluge," he said, adding that people had already fled the towns, parts of which were under three metres of water.

"The flood waters are now heading to the Arabian Sea."

Authorities have struggled to feed, house and arrange medical care for the survivors of the floods. Foreign countries and the United Nations were slow to respond to the disaster, in part because it took a long time for its extent to become clear.

Aid is slowly reaching the worst-affected areas by army helicopter, road and boat, but millions have received little or no help. The United Nations warned that additional funding for emergency food was urgently needed to ensure supplies into next month.

Once all the flood waters recede, the country will be left with a massive relief and reconstruction effort that will cost billions of dollars and take years. An estimated one million homes have been damaged or destroyed, five times as many as were hit by this year's earthquake in Haiti.