"We know where [the kidnappers] are ... and we are discussing their terms"
Mutrif Siddig, foreign ministry undersecretary
The five were working for Belgian MSF when they were seized by men in Serif Umra.
Earlier on Friday, Koen Baetens, a spokesman for MSF, said the trio were in good health.
MSF pulled nearly all of its personnel out of Darfur and into the capital, Khartoum, following the abductions. Only staff working on securing the release of their colleagues have remained behind.
The attack on the Belgian MSF branch came days after the French and Dutch contingents of the aid organisation were told to leave Darfur.
The Belgian foreign ministry said that none of its nationals was involved.
MSF branches are among 13 aid groups ordered to leave Sudan after the International Criminal Court (ICC) issued an arrest warrant for Omar al-Bashir, Sudan's president, for alleged war crimes in Darfur.
Khartoum accuses the aid groups of co-operating with the ICC, which says that al-Bashir led a violent campaign in Darfur over the past six years.
The United Nations says that more than 180 foreign aid workers have left Sudan since the order by Khartoum to expel the aid groups.
The World Food Programme (WFP) says four of its partner relief agencies expelled from Darfur were looking after 35 per cent of food distribution to the region.
The UN estimates that about 300,000 people have died in Darfur from the combined results of war, famine and disease over the course of the last six years and at least 2.7 million have been displaced.
The conflict in Darfur erupted after ethnic fighters rebelled against the Arab-dominated government.