Ferrero-Waldner said she was "extremely concerned" about the future of the BHS, which is one of Belarus's leading rights groups.
The January 29 move threatens the legal existence of the group, as it deprives it of a legal address.
Ferrero-Waldner called on Belarusian authorities to immediately cease what she called the "harassment" of the group and to respect the rights of NGOs.
She recalled that the EU's offer to engage in a close relationship with Belarus as a partner within the European Neighbourhood Policy is subject to Belarus "taking steps towards democratization and respect for human rights."
On January 29, the United States also denounced the Belarusian authorities' decision.