Country director Paul Barker became the third prominent foreign official ordered out of Sudan since last week.
"We are deeply disappointed by the decision of the government of Sudan," CARE's chief executive officer, Helene Gayle, said in a telephone interview.
Gayle said Sudan had ordered Barker to leave within 72 hours, without explaining why, and he was complying. Sudanese government officials did not return phone calls seeking comment.
Gayle that Sudan may have misinterpreted what she called standard international communications about staff safety in the country. She did not elaborate.
Barker "has not said or done anything that would be inappropriate," she said.
CARE has 600 people in Sudan, where it has spent $184 million on aid projects over 27 years, Gayle said. The organization has spent $60 million, mostly in Darfur, over the last three years, she said.
"We hope to resolve this issue so that CARE can continue its long-term role in delivering humanitarian assistance to the people of Sudan," Barker said.
Many Western countries and international organizations have been critical of the Sudanese government's role in Darfur. CARE has not.
Sudan expelled the top Canadian diplomat and the European Commission envoy last week for what was described as "meddling in its affairs," without further explanation. The Sudanese government later said that the EU official, Kent Degerfelt, could serve out the remaining three weeks of his mandate as long as he was replaced by someone new.
More than 200,000 people have died in Darfur since ethnic African rebels took up arms against the Arab-dominated central government in 2003, accusing it of discrimination.
Khartoum is accused of retaliating by unleashing militias known as the janjaweed, which are blamed for the worst atrocities against civilians in a conflict that has displaced more than 2.5 million people.
"Throughout Sudan, the critical humanitarian work of NGOs, including CARE, along with all U.N. humanitarian agencies and partners, needs the active support and facilitation of the Sudanese government," U.N. spokeswoman Michele Montas said in New York.