Vice-President Ali Osman Taha told reporters on 4 March that several relief groups had been asked to leave because "they are breaking the law of the country".
Taha did not elaborate, but added that Sudan remained "committed to the implementation of the agreement we signed with the UN and other NGOs".
The expelled organisations include Oxfam, CARE, MSF-Netherlands, Mercy Corps, Save the Children, the Norwegian Refugee Council, the International Rescue Committee, Action contre la faim, Solidarités and CHF International.
Sources said the groups received notice to leave after the International Criminal Court (ICC) issued an arrest warrant for President Omar el-Bashir on war crimes charges.
Bashir denies all the charges, describing them as "not worth the ink they are written in".
"Shortly after the announcement, Sudan's government revoked the registration of several aid agencies, including Mercy Corps," Neal Keny-Guyer, its chief executive officer, said. "We plan to appeal the decision under Sudanese law."
The expulsion of NGOs will, however, not apply to the semi-autonomous Southern Sudan, which is slowly rebuilding after more than two decades of war with the North - unless the government there decides so, sources said.
"We were told we have 24 hours to leave, that we simply must just go," said one NGO official, who requested anonymity. "It doesn’t seem we have any choice but to comply."
The removal of key agencies would be a severe blow to the poorest, especially in the western region of Darfur where violence has displaced several million from their homes, observers said.
|We were told we have 24 hours to leave, that we simply must go...It doesn't seem we have any choice but to comply|
UN Secretary-General Ban Ki-moon warned that the decision represented "a serious setback to lifesaving operations in Darfur" and called on the government to reverse it.
Two Sudanese organisations, the Khartoum Centre for Human Rights and Environmental Development and the Khartoum Amal Center for the Rehabilitation of the Victims of Violence, were also reported on 5 March to have been shut down.
The revocation of Oxfam's licence would affect more than 600,000 Sudanese people who have been receiving humanitarian and development aid, Penny Lawrence, Oxfam's international director, said.
"Oxfam does not have an opinion on the [ICC's] activities, and our sole focus is meeting humanitarian and development needs in Sudan," it said in a statement.
The IRC was ordered to close its humanitarian aid programmes in Darfur as well as North and East Sudan. The decision, it stated, had put 1.75 million people at risk.
Photo: Derk Segaar/IRIN
|Displaced women returning to a camp in Darfur after collecting firewood (file photo)|
CARE said it had received a letter from the government cancelling its registration to operate in Sudan and was assessing the implications for its 1.5 million beneficiaries.
Save the Children said the decision by Sudanese authorities to suspend its operations would affect 50,000 children in Khartoum and the northeast. Many of these children, said Ken Caldwell, director of international operations, were living in camps, having been forced to flee their homes by the ongoing conflict.
In February, government officials warned several aid agencies to avoid involvement in Sudanese politics, and accused them of working with their own governments against Khartoum.
"We know that some NGOs are governmental," Humanitarian Affairs Commission chief Hassabo Mohammed Abdel Rahman said at the time. "We see in practice and implementation more involvement of politicians, either ambassadors or governments within these NGOs."
A day after the ICC announcement, Sudanese officials were in a defiant mood as thousands of Bashir supporters staged a massive demonstration in Khartoum.
"We are concerned this may expand to others," said another aid official in Khartoum, who declined to be named. "We are nervous of the future."