Foreign Minister Mustafa Osman Ismail did not elaborate, but his statement on Wednesday raised expectations that charges will be dropped against the employees of Medecins Sans Frontieres (MSF), who were arrested after their agency spoke of alleged rape cases in the troubled western region of Darfur.
Ismail said an agreement had been reached that would "allow the voluntary agencies to operate and work professionally within the humanitarian framework and would at the same time preserve the respect and national will of the country", the official Sudan News Agency reported.
A spokeswoman for the UN mission in Sudan could not be reached for comment, and MSF said it had not received any new information from the Sudanese authorities about the two men.
On Monday, MSF's head in Sudan, Paul Foreman, was arrested and charged with spreading false information.
The next day a Dutch worker with the group, Vincent Hoedt, was arrested in Darfur, the group said. Both men were later released on bail.
The arrests came after MSF issued a report in March saying its doctors working in Darfur had collected medical evidence of 500 rapes over four and a half months.
The report said more than 80% of the victims reported that their attackers were soldiers or members of government-allied militia. Sudan's government denied the claims.
"Organisations operating in Sudan should observe the country's national security in their dealings and they should not be seek to tarnish Sudan's image through issuance of false information"
Mustafa Osman Ismail,
Sudan Foreign Minister
However, the UN mission in Sudan said on Tuesday that in response to allegations of sexual abuse by government troops the Sudanese government "has issued a directive to the military commanders in different locations that serious action will be taken against them if found implicated in such acts".
The Dutch government summoned the Sudanese ambassador to protest against the arrests, and the UN also complained.
UN Secretary-General Kofi Annan's special representative to Sudan, Jan Pronk, said on Wednesday that he backed the MSF report on rapes in Darfur "100%".
Earlier on Wednesday, Ismail had warned international organisations not to meddle in his country's affairs.
"Organisations operating in Sudan should observe the country's national security in their dealings and they should not seek to tarnish Sudan's image through issuance of false information," he said.
UN envoy Jan Pronk says he
backs the MSF claims 100%
More than two years of conflict in Darfur has killed at least 180,000 people, many from war-induced hunger.
The conflict erupted when tribes in the western region took up arms against what they saw as years of state neglect and discrimination.
The government is accused of responding with a counterinsurgency campaign in which government-backed militiamen known as Janjawid committed wide-scale abuses - including killings, rape and arson - against the population.