Holmes, who is on his first tour of the region since taking up office, met delegates of international aid groups on Saturday and Sunday as part of his two-day visit to Darfur.
 
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He said problems such as obstruction from Sudan's government and insecurity on the ground have created an environment where "morale is fragile" and could push aid workers to pull out.
 
"The risk is high," he said. "It is not imminent, but if things deteriorate, people may not want to maintain their efforts."
 
Es Sallam, the refugee camp visited by Holmes and where some 45,000 people have taken refuge from the region's spiraling violence, is one of three camps near El Fasher.
 
Holmes said people in the camp were not starving and health conditions seemed decent.
 
But the camp is over spilling with people and aid workers are currently negotiating space for a fourth camp to meet the incoming flow of refugees.
 
Sanctions
 
The UN has already imposed sanctions on Sudan in a bid to curb violence in the region.
 
Speaking on the sidelines of the EU's 50th birthday celebrations in Berlin, Tony Blair, the British prime minister, said sanctions against Sudan should be extended through a new UN Security Council resolution.
 
"It is essential for the international community to take a new resolution on Darfur in the Security Council," Blair said.

"The issue is, we need to get a new resolution to extend the  sanctions regime against key individuals."
 
He also suggested a no-fly zone over Darfur.
 
"We need to consider in my view a no-fly zone," he said.
 
Earlier, Angela Merkel, the German chancellor, had urged her EU counterparts to back tougher sanctions against Sudan.
 
"I want to state frankly that we have to consider stronger  sanctions," she said.
 
People in need of aid
 
About 4 million people in Darfur are in need of aid. The UN says they have been caught in the midst of fighting between armed groups, government forces and the pro-government janjawid.
 
More than 200,000 people have been killed and more than 2 million displaced in four years of fighting, with the Arab janjawid accused of widespread atrocities against ethnic African civilians.
 
Holmes had been turned away from the camp on Saturday by Sudanese military police when he tried to visit on Saturday.
 
On Sunday, the governor of north Darfur extended apologies to Holmes for the incident.
 
The UN humanitarian chief said he accepted the apology but would nonetheless raise the issue with Sudanese officials because it illustrated the problems faced by relief workers trying to deliver aid to Darfur's population.
 
The international aid effort in Darfur is the largest in the world with over US $1bn spent and some 14,000 aid workers active in the region.