The United Nations refugee agency (UNHCR) and officials at the Sahrawi refugee camps said on Tuesday that rains had washed away many of the mud-brick houses where some 158,000 refugees have been living since fleeing the disputed Western Sahara territory.
A spokesman for the Western Sahara's independence movement, the Polisario Front, told Reuters in Algiers: "Heavy rains over the past few days destroyed 50% of shelters."
UNHCR said 50,000 refugees had been left homeless and it was preparing to send relief supplies to the camps.
In a website statement, the UNHCR said: "An airlift currently being arranged will deliver lightweight tents, blankets, jerry cans, mattresses and plastic sheeting from our regional warehouse in Jordan."
The Sahrawi Red Crescent said the situation was worsening, and urged donors and international organisations to speed up their efforts as food stocks dwindled.
The Red Crescent said: "We launch this emergency call to relieve thousands of women, children and elderly people. We urge donors to intervene as soon as possible to rebuild schools and hospitals."
The conflict in Western Sahara was triggered by Morocco's seizure of the northwest African desert territory shortly after former colonial power Spain withdrew in 1975.
The Polisario Front, whose principal backer is Algeria, fought a 16-year guerrilla war with Morocco.
The UN brokered a ceasefire in 1991 with the promise of a referendum on the territory's future, but Morocco has refused to allow a vote on self-determination.