LOS ANGELES – The Vatican has ordered an overhaul of the most important group of nuns in the United States after an investigation found what Roman Catholic Church officials called “radical feminist themes” that questioned official positions on homosexuality and the ordination of women.

In a bluntly worded report, the Vatican’s watchdog of orthodoxy, the Congregation for the Doctrine of the Faith, found what it called “serious doctrinal problems” with the Leadership Conference of Women Religious, based in Silver Spring, Md.

The Vatican on Wednesday named Archbishop Peter Sartain of Seattle to oversee changes in the group.

The Leadership Conference, which says it has more than 1,500 members representing more than 80 percent of the 57,000 women religious in the United States, stated it was “stunned” by the official assessment.

“This is a moment of great import for religious life and the wider church,” the group said in a statement posted on its website. “We ask your prayers as we meet with the LCWR National Board within the coming month to review the mandate and prepare a response.”

The Vatican’s actions come at a time when Rome appears to be reasserting its conservative vision over some elements of the church, particularly in the United States.

Nuns have questioned a variety of church positions, including the ban on ordaining women. In 2010, American bishops opposed the Obama administration’s health care insurance overhaul, but some nuns were very visible in supporting the plan.

In its assessment of the Leadership Conference, the Vatican cited letters from some in the group “protesting the Holy See’s actions regarding the question of women’s ordination and of a correct pastoral approach to ministry to homosexual persons.”

“The terms of the letters suggest that these sisters collectively take a position not in agreement with the Church’s teaching on human sexuality. It is a serious matter when these Leadership Teams are not providing effective leadership and example to their communities, but place themselves outside the Church’s teaching,” the report said.

The Vatican also “noted a prevalence of certain radical feminist themes incompatible with the Catholic faith in some of the programs and presentations sponsored by the LCWR, including theological interpretations that risk distorting faith in Jesus and his loving Father who sent his Son for the salvation of the world. Moreover, some commentaries on ‘patriarchy’ distort the way in which Jesus has structured sacramental life in the Church; others even undermine the revealed doctrines of the Holy Trinity, the divinity of Christ, and the inspiration of Sacred Scripture.”

The Congregation for the Doctrine of the Faith is now led by Cardinal William Levada, formerly the archbishop of San Francisco. Pope Benedict XVI headed the office until 2005.

The investigation of the American women religious began in 2008; when it was announced, some nuns and their backers complained that it was an attempt to rein in their communities, which often provide key social services in schools and hospitals.

Despite its strong language questioning the nuns on doctrine, the report praised their work: “The Holy See acknowledges with gratitude the great contribution of women Religious to the Church in the United States as seen particularly in the many schools, hospitals, and institutions of support for the poor which have been founded and staffed by Religious over the years.”