MSF-Holland's head of mission in Sudan, Paul Foreman, and its regional co-coordinator in Darfur, Vincent Hoedt, were arrested at the end of May and charged with publishing false information, undermining the Sudanese society and spying.
The charges were related to the publication in March of a report entitled "The Crushing Burden of Rape" - on sexual violence in the strife-torn western region of Darfur. The two officials had been freed on bail and forbidden to leave the country.
"The charges were dropped yesterday (Sunday) and this morning [Monday] were received the confirmation," James Lorenz, MSF's spokesman in the Kenyan capital, Nairobi, told IRIN.
"MSF operations in Sudan will continue just as they have during the past couple of years," he added.
The general director of MSF-Holland, Geoff Prescott, welcomed the dropping of the charges.
"Hopefully we will be able to again focus all our attention on providing humanitarian assistance to the victims of the conflict in Darfur, most of whom are entirely dependent on aid," Prescott said in a statement.
"The people in Darfur are still suffering from violence and extreme medical needs and MSF will continue to stand by them," he added.
The Sudanese government was angered by the report which said MSF doctors working in Darfur had collected medical evidence of 500 rapes over four-and-a-half months.
More than 80 percent of the victims said their attackers were soldiers or members of government-allied militia. The report did not accuse the government of Sudan.
Faced with hundreds of women and girls seeking medical care following rape and sexual violence in Darfur, MSF said it published the report in order to raise awareness about the ongoing violence against women.
The war in Darfur pits Sudanese government troops and militias - allegedly allied to the government - against rebels fighting to end what they have called marginalisation and discrimination of the region's inhabitants by the state.
Over 2.4 million people continue to be affected by the conflict, 1.86 million of whom are internally displaced or have been forced to flee to neighbouring Chad.