Fifty people were injured and about 1,000 made homeless in the town, a UN World Heritage site, 600km south of the capital, Algiers, at the entrance to the Algerian desert in the M'Zab valley.
Ahmed Ouyahia, the prime minister, gave "strict orders for victims of the natural catastrophe to be taken care of by releasing" unrestricted funds, Djamel Ould Abbas, the minister for national solidarity said on Friday.
The interior ministry sent tents, generators and 400 tonnes of first aid, but residents said they needed emergency supplies more quickly.
|Residents prayed during their protest for faster assistance [EPA]
State radio said the water level was eight metres high in some parts of the town.
Noureddine Yazid Zerhouni, the interior minister, said the floods were the worst in the country for a century. Residents reported sweeping damage.
A resident of El-Gaba, a village near Ghardaia, said: "Hundreds of houses have been destroyed but thousands have been damaged and are uninhabitable in the area.
Another resident said four people from the village had died and three others were missing in the "unimaginable catastrophe".
One resident said nearly all the homes would have to be rebuilt. Gas and electricity supplies have been partially restored.
Several parts of Algeria were lashed by heavy rain including Djelfa - midway between Ghardaia and Algiers - where two people were killed.
Flooding in the Algiers region in 2001 killed more than 800 people and caused considerable damage.