The Rev. J. Gaston Hebert, the diocese administrator, said he notified the nuns of the decision Tuesday night after they refused to recant the teachings of the Community of the Lady of All Nations, also known as the Army of Mary.
The Vatican has declared all members of the Army of Mary excommunicated. Hebert said the excommunication was the first in the diocese's 165-year history.
"It is a painfully historic moment for this church," Hebert said.
The six nuns are associated with the Good Shepherd Monastery of Our Lady of Charity and Refuge in Hot Springs. Sister Mary Theresa Dionne, one of the nuns excommunicated, said the nuns will still live at the convent property, which they own.
"We are at peace and we know that for us we are doing the right thing," the 82-year-old nun said. "We pray that the church will open their eyes before it is too late. This is God's work through Mary, the blessed mother, and we're doing what we're asked to do."
At a news conference, Hebert said the nuns "became entranced and deluded with a doctrine that is heretical." He said church officials removed the Eucharist - which Catholics revere as the body of Christ - from the monastery on Tuesday night.
Hebert said the sect's members believe that its 86-year-old founder, Marie Paule Giguere, is the reincarnation of the Virgin Mary and that God speaks directly through her.
Excommunication bars the nuns from participating in the church liturgy and receiving communion or other sacraments.
The diocese said the action was taken after the Congregation for the Doctrine of the Faith issued a declaration dated July 11 that the Army of Mary's teachings were heretical and automatically excommunicated any who embraced the doctrine.
Hebert said the diocese had known for years that the nuns were following the sect and said church officials in the past had encouraged them to come back into the fold.
According to the Catholic News Service, the Army of Mary was founded in Quebec in 1971 by Giguere, who said she was receiving visions from God.
Dionne said she does not know if Giguere is the reincarnation of the Virgin Mary, but said she believes God communicates through the sect's founder.
"She is doing only what God and Mary tells her to do," Dionne said.
A spokesman for the Army of Mary called the excommunication of the nuns and the other members of the sect an injustice. Father Eric Roy said Giguere has not claimed to be the reincarnation of the Virgin Mary, and said the 86-year-old Quebec woman "receives graces" from the Virgin Mary and God.
"The Virgin Mary took possession of her soul. I would rather say it that way," said Roy, superior general of the Sons of Mary, an associated group.