The two aid workers were allegedly seized after men overpowered security guards, ACF said.
"Some gunmen trussed [up] the ACF guards in front of the guesthouse and then went into the house. They kidnapped the two expatriates present in the house at that time, and ran away with several vehicles," it said.
Sultan Ali Uruzgani, the governor of Day Kundi, said: "The two aid workers working for Action Against Hunger were kidnapped by the enemies of Afghan government."
ACF said it was doing its utmost "to [secure] their release as rapidly as possible and in the best conditions".
A crisis group has been set up in Kabul and Paris to help win their release, ACF said.
The French foreign ministry said in a statement that it was "mobilising, in Paris as well as Kabul, to obtain their release as quickly as possible".
It said that the "targeting of humanitarian personnel is totally unacceptable" while promising "discretion" in its efforts to free the duo.
France has 1,600 troops serving in a Nato-led force in Afghanistan fighting the Taliban and is planning to deploy more troops in the coming months.
ACF, who set up its first office in Afghanistan in 1979, from where it has conducted a series of operations since 1995, said it has suspended all its relief operations in the country following the incident.
The abduction comes after the kidnapping in May of a French businessman, who was released last month after weeks of behind-the-scenes negotiations.
Last year, two French humanitarian workers for the Terre D'Enfance (A World For Our Children) relief group were released, several weeks after their abduction amid much speculation that a ransom had been paid.