She did not elaborate.
"The United Nations is extremely concerned about the ramifications of this decision," said Marie Okabe, a UN spokeswoman.
Okabe said the expulsion violated agreements signed between the UN and the Sudanese government to facilitate aid in Darfur.
She also said that Ameerah Haq, the chief UN humanitarian co-ordinator in Sudan, was taking up the issue with authorities in Khartoum, the Sudanese capital.
UN officials have said that the state governor's directive in Darfur accused al-Haj-Ibrahim, a Canadian of Palestinian descent, of violating "rules of humanitarian action," but did not specify how he had had done so.
The Aegis Trust, a British-based group that campaigns against genocide, said al-Haj-Ibrahim had been forced out for "resisting a policy that amounts to further ethnic cleansing" of Darfur's African population.
James Smith, Aegis chief executive, said: "With no security to allow them to return home and rebuild, forced removal of the [displaced people] from the camps gives their inhabitants no choice but to leave the region or die."
Both UN aid officials and independent charities working in Darfur have complained of bureaucratic harassment by Sudanese authorities.