The report has been confirmed by France's Foreign Ministry, which said a crisis unit would be sent to the area to negotiate the hostages' release.
The Paris-based aid group, which has been working in Afghanistan since 1979, said it has suspended activities in the country following the abductions.
The group said the two aid workers were taken at the house they were staying at, in the town of Nili. The gunmen reportedly tied up security guards and made off in several cars.
No militant group has yet claimed responsibility for the kidnapping.
France has around 1,500 troops fighting the Taliban-led insurgency in Afghanistan.
The Taliban has vowed to step up terrorist attacks in the country. More than 6,000 people were killed in violence in Afghanistan during 2007, nearly 2,000 of them civilians, according to official sources.
