Uzbekistan's Justice Ministry has accused the organization of breaking a number of laws.
Lelei LeLaulu, the head of Counterpart International, told RFE/RL's Uzbek Service that the group has not decided whether it will lodge an appeal.
"There is a certain point where we have to look and decide whether an appeal will only make it more difficult for our staff and colleagues or whether we should just accept the court's order at this stage and perhaps look at ways of working with the Uzbek people in another stage of our development," LeLaulu said.
In a statement on May 3, Counterpart International said it has delivered nearly $80 million in medical and humanitarian aid during its work in Uzbekistan.
In the past six months, Uzbek authorities have also shut down offices of the UN High Commissioner for Refugees, the group Freedom House, and Radio Free Europe/Radio Liberty's Tashkent bureau.