"The suspension applies for all of Darfur and this will continue until we get an explanation," Jamal Ibrahim, Sudan's foreign ministry spokesman, said on Sunday.
He said the ban, which excludes two bodies affiliated to the UN mission - the World Food Programme and Unicef, the UN children's agency - was imposed because a UN helicopter had moved Suleiman Adam Jamous, who rejects a peace deal signed on May 5.
After three years of revolt in Sudan's remote west, tens of thousands of people have been killed and 2.5 million forced into camps, creating one of the worst humanitarian crises and sparking the world's largest aid operation.
Only one of the three rebel factions negotiating in the Nigerian capital Abuja signed the African Union-mediated deal and tens of thousands in Darfur have demonstrated, at times violently, against it.
They say it does not meet their basic demands of proper compensation for war victims or enough political posts and the rebels want to monitor the disarmament of pro-government militias, known locally as Janjawid.
'Sudan not consulted'
Jamous was the humanitarian coordinator for the main rebel Sudan Liberation Army (SLA) before it split in November last year. He was the main contact for the more than 14,000 aid workers in the region.
"He was picked up by the UN helicopter between el-Fasher and Musbat," Ibrahim said, referring to areas in North Darfur.
"The authorities were not consulted, no permission was asked for and it was clear negligence"
Sudanese foreign ministry spokesman
"The authorities were not consulted, no permission was asked for and it was clear negligence," he said, adding it was a "flagrant violation" of the sovereignty of Sudan.
Minni Arcua Minnawi, the leader of the SLA faction who signed the deal, had imprisoned Jamous for his opposition to the deal, rights groups and other rebel leaders said.
UN officials and other rights groups had been involved in securing his release.