The Vatican has said the Leadership Conference of Women Religious violated church teaching on birth control and homosexuality, among other issues.
The group made the announcement at the end of a national meeting.
Church officials have appointed three US bishops to oversee an overhaul of their organisation.
LCWR is the largest organisation of nuns in the US, representing 80% of the 57,000 nuns in the United States.
'Starting point'Sister Pat Farrell, the group's leader, said they would continue discussions with the bishops "as long as possible, but will reconsider if LCWR is forced to compromise the integrity of its mission".
The board will first meet with Seattle Archbishop Peter Sartain, to begin what is said to be a five year process.
"Dialogue on doctrine is not going to be our starting point," Sister Farrell said. "Our starting point will be about our own life and about our understanding of religious life."
Representatives from both sides met in June, after a Vatican report accused the nuns of adopting "certain radical feminist themes".
The nuns, who say they have been unjustly criticised, returned to the US at the end of the talks to decide what to do next.
The BBC's David Willey in Rome says that despite the Vatican's hopes for constructive talks, the nuns have shown little desire for compromise.
They were understandably hurt, he said, at being told to mend their ways by the Vatican at a time when the US Church has lost credibility over sexual abuse scandals involving priests.
The nuns also knew they had the support of many ordinary Catholics in the US, who had been organising vigils outside churches.
After the report was released, there were protests outside the Vatican embassy in Washington, and over a hundred members of the US Congress sponsored a resolution to commend the nuns for their service.
