"It did not come from Khartoum and we are handling the matter with the state authorities [of West Darfur]," Mutrif Siddiq, the minister of state for humanitarian affairs, told the AFP news agency.
Aid organisations claim expulsions are often the punishment for anyone reporting on human rights abuses during the seven-year Darfur violence.
Khartoum says some international workers go beyond the purpose of their mission in Sudan.
It claims an International Criminal Court (ICC) war-crimes arrest warrant against Omar al-Bashir, the Sudanese president, is largely based on information that came from international workers in the country.
Thirteen aid organisations have been expelled from Sudan since the ICC issued the warrant for al-Bashir last year.
"The heads of the UNHCR (UN refugee agency) and FAO (UN food and agriculture agency) agencies in West Darfur as well as the head of UNHCR agency in Zalengei have been asked to leave," said al-Fadil.
"The government also informed me that it had asked both the ICRC's heads of delegation in el-Geneina and Zalengei to leave too," he added.
The ICRC said its staff had been "recalled with the agreement of authorities" and added that its operations continued as normal in West Darfur.
Another UN source, who declined to be named, said the FAO head of office in West Darfur was told to leave because he had forwarded a petition against hunger - www.1billionhungry.org - and authorities had said he did not obtain approval for it.
On August 7, al-Bashir told the three Darfur governors they could expel any foreigner who failed to respect Sudan's authority.
Unamid is in a tense standoff with Darfur authorities over sheltering six refugees from the volatile Kalma camp, who the government says are responsible for violence which killed eight people last month.
The peacekeepers say that without an arrest warrant or guarantees of a fair trial they will not hand over the refugees.
Kidnappings of foreign aid workers and Unamid staff began last year after the ICC warrant for al-Bashir was issued.
On Saturday two Jordanian Unamid police were abducted, while a US woman from the Samaritan's Purse charity was taken three months ago.
The kidnappers are usually young men from Arab tribes who demand ransom money.
Sudan has yet to prosecute any of the abductors.