The national board of the nuns' group issued the statement, its first since the Holy See ordered the overhaul, after a three-day private meeting.
"Board members concluded that the assessment was based on unsubstantiated accusations and the result of a flawed process that lacked transparency," the statement said. "Moreover, the sanctions imposed were disproportionate to the concerns raised and could compromise their ability to fulfill their mission."
The Vatican reprimand prompted an outpouring of support for nuns by Catholics and non-Catholics. Vigils, protests and prayer services defending the sisters have been held nationwide, including outside the U.S. embassy of the Holy See in Washington.
"The report has furthermore caused scandal and pain throughout the church community, and created greater polarization," the board said.
In an interview, the president of the organization, Sister Pat Farrell, declined to comment on specifics of the report or go into detail about what the group considers the flaws in the findings. She said the organization would formally respond to the investigation after discussions with members at regional meetings and a national assembly in August.
"The mood at the board meeting was one of deep, deep sadness about this document that has come from the Vatican, but there was also a spirit of deep prayer and reflection and sincere searching together," Farrell said. "It is a concern of ours that we would be faulted for what we don't say. I don't think we're talking about a matter of orthodoxy but a matter of emphasis."
The meeting in Rome is planned with Cardinal William Levada, an American who leads the congregation, and Seattle Archbishop Peter Sartain, appointed by the Vatican to take authority over the group. Sartain will oversee rewriting the group's statutes, reviewing all its plans and programs including approving speakers and ensuring the organization properly follows Catholic prayer and ritual.
Farrell has been a sister for 47 years. She said she was "stunned at the severity" of the reprimand.
"I didn't think I would ever see anything like this," Farrell said. "Truthfully, I'm glad my mother is not alive to see this unfolding. She would be heartbroken."