The group's board met in Washington to discuss the report, CNN said. The Vatican in April accused the organization of inviting "radical feminists" to speak at the annual meeting, working for social justice while neglecting issues like same-sex marriage, abortion and euthanasia.
The board said its leaders plan to go to Rome for discussions with the Congregation of the Doctrine of the Faith.
The report "was based on unsubstantiated accusations and the result of a flawed process that lacked transparency," the board said. It also "caused scandal and pain throughout the church community and created greater polarization."
The sanctions imposed by the Vatican are too severe, the group said, and would keep nuns from carrying out their mission.
The conference represents about 80 percent of nuns in the United States.