Flooding following rare torrential rains on the edge of the Algerian desert have killed at least 30 people and injured 50, while damaging hundreds of homes, officials said.

Algeria's Interior Minister Noureddine Yazid Zerhouni said the floods are the worst for a century and warned of higher casualties in Ghardaia, some 600 kilometres south of Algiers in the M'Zab Valley, a UN World Heritage site.

"Based on the overflight that we made, the toll unfortunately could be greater," Zerhouni told reporters after meeting local authorities in the region, which links the High Plateau area with the Sahara.

Rain had been falling since Monday in the region.

The government previously said 13 people had been killed in the floods, which have damaged some 600 homes, many of them in oasis areas.

A local resident reached by telephone by AFP suggested the toll could indeed be higher in the Algerian region following the first rainfall in four years.

"The population even talks of about a hundred victims and up to one thousand houses flooded," he said, while adding that the rainfall, which began Monday and continued Tuesday, had become "a deluge".

The resident also said seasonal rivers had filled up and spilled into a larger one, which then flooded, sweeping away everything in its path.

Several areas in Algeria were lashed by heavy rain over two days including Djelfa - midway between Ghardaia and Algiers - where two people died.

Meanwhile a journalist for radio station Chaine 3 described the floods as an "incomparable catastrophe."

"It is like nothing I have seen before. There was up to eight metres of water in the town's narrow back streets and residents of Ghardaia palm grove have had to seek refuge on the houses' terraces or anywhere high up," he said.

The flooding has also cut off roads and rendered telephone connections erratic.

"The bakeries are shut, there is neither gas nor electricity, the shops are flooded and their stocks are probably unusable," Zerhouni said, adding the government's priority was to aid the affected population.

Ministers met in Algiers to assess the damage and the population's needs, a government source said.

The army helped deliver by air some of the first aid deliveries, which include more than 400 tonnes basic food supplies, 200,000 blankets, a thousand tents, three mobile bakeries, 50 generators and water purification equipment.

It also began imposing security checks in the affected areas to prevent looting, the local governor said.

Algeria is no stranger to bad weather, particularly in the north. Flooding in the Algiers region in 2001 killed more than 800 people and caused considerable damage.