"We were informed yesterday by the Ministry of Foreign Affairs that all the charges have been dropped because of all our good medical work in Sudan," MSF official Kenny Gluck said in Khartoum on Monday.
MSF Holland's country director Paul Foreman and Darfur chief Vincent Hoedt were arrested last month after the aid group published a report detailing some anonymous testimonies of 500 rape victims over four and a half months in the troubled Darfur region.
The report was based on medical evidence after the victims were treated in MSF hospitals in the remote region.
The government says there are few rape incidents in Darfur, despite evidence found by a UN-appointed commission of inquiry of mass rape and reports by human rights groups and non-governmental organisations of widespread rape.
The International Criminal Court launched an investigation this month into alleged crimes against humanity during more than two years of rebellion in Darfur.
It has a list of 51 senior government and military officials, rebel and militia leaders and foreign army officers suspected of war crimes.