The decision took the aid workers by surprise, secretary general Elisabeth Dahlin tells Swedish Radio.
"We were told two days ago that we had to be out of the area by the end of June," she says.
"What is important to us now is to find out why and initiate a dialogue. We can't speculate about anything because we have no information right now," says Dahlin.
She says they work with local and county level politicians and have received good feedback from the central government.
The organisation has 15 employees in the eastern part of Sudan helping children get access to schooling.
Two Irish and one Japanese aid organisation have also been ordered to leave, reports the news agency TT.