"It's a major concern," a U.N. spokesman said. "They (the south Sudanese authorities) promised to stop, but the demolitions continued."
South Sudan's capital Juba has had uncontrolled growth since the mainly Christian and animist region ended its two-decade civil war with the mostly Muslim north in 2005.
A peace created a southern parliament and gave the region a share in the country's oil revenues.
The return of relative stability brought thousand of people pouring back into the former garrison town, transforming it into a bustling commercial centre.
In recent months, authorities from the surrounding Central Equatoria state have sent in bulldozers and demolition crews to flatten of hundreds of temporary structures, market stalls and shanty town shacks that they said were not properly licensed.
The U.N. issued a report this week many people had not received proper warning before their properties were demolished, or enough compensation afterwards.
UNMIS, the peacekeeping operation mandated to watch over the implementation of the fragile north-south deal, has called for the government to halt the demolitions and to provide services, land and compensation to those who have lost their homes.
"UNMIS is concerned that implementation of the Government of Central Equatoria's plan to improve living conditions in Juba has not been done in a manner which is consistent with southern Sudanese law and international human rights standards," it said.
A member of Central Equatoria state's parliament, Jacob Aligo, told Reuters most owners of unlicensed properties had been given ample warning before demolition started.
"(But) some mistakes were committed, many were not provided with alternative means," he said
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