A US Catholic nuns' group said it is "stunned" that the Vatican reprimanded it for spending too much time on poverty and social justice concerns and not enough on abortion and gay marriage.
The Vatican said the Leadership Conference of Women Religious had been "silent on the right to life".
It also said the group had failed to make the "Biblical view of family life and human sexuality" a central plank in its agenda.
It further reprimanded US nuns for expressing positions on political issues that differed, at times, from views held by US bishops.
Public disagreement with the bishops - "who are the church's authentic teachers of faith and morals" - is unacceptable, the report said.
The Vatican's Congregation for the Doctrine of the Faith issued a "doctrinal assessment" saying the Holy See was compelled to intervene with the Leadership Conference of Women Religious to correct "serious doctrinal problems."
The nuns' group said in a statement on its website: "The presidency of the Leadership Conference of Women Religious was stunned by the conclusions of the doctrinal assessment."
It added that the group may give a lengthier response at a later date.
The conference said it represented 80% of America's 57,000 Catholic nuns and is influential both in the US and globally.
Academics who study the church said the Vatican's move was predictable given Pope Benedict's conservative views and efforts by Rome to quell internal dissent and curtail autonomy within its ranks.
University of Notre Dame historian Scott Appleby said that "this is more an expression of the Church feeling under siege by trends it cannot control within the Church, much less within the broader society," including a steady drumbeat of calls to ordain women as priests, which the pope has reasserted was an impossibility.
The Vatican named Seattle Archbishop Peter Sartain and two other US bishops to undertake the reforms of the conference's statutes, programmes and its application of liturgical texts, a process it said could take up to five years.