The American singer wants to buy their convent as her new home, but the nuns claim they have already sold the property to a restaurateur.
The Archdiocese of Los Angeles and the Sisters of the Immaculate Heart of Mary went to court to argue who should be able to sell it, after the Archdiocese claims the Church and Vatican owns it and the sisters have no right to sell it.
The nuns claim they sold the property to Los Angeles restaurateur, Dana Hollister, for around $15.5 million (around £9.9 million).
Sister Rita Callanan, 77, and Catherine Rose Holzman, 86, say they object to the singer buying the convent because they do not agree with her music, including hits like "I Kissed A Girl".
The Judge, James Chalfant, asked why the Archbishop had power to choose the buyer, he replied: "He got it (authority) from the Pope!"
"There are clear canons saying the Pope administers ecclesiastical properties.
"The Hollister sale is clearly invalid.
"The archbishop and archdiocese have the right to sell the property, which benefits the sisters.
"This is a problem for the sisters because they don't trust the archdiocese."
The judge stressed that he cannot authorise the sale to Katy Perry, that hearing will take place in October.
The judge told lawyers for the archdiocese: "You're not selling to Katy Perry any time soon."
It has also been reported the judge said no one wanted to live there apart from Katy Perry, according to The Telegraph.
Katy Perry's lawyer offered in court to begin paying rent on the property immediately and presented documents from the Archbishop authorising the sale to Miss Perry.
Perry's offer was also to pay in cash immediately, whereas lawyers say Miss Hollister will pay $44,000 (£28,000) with a promise to pay the rest later.
Lawyers also accused Hollister of taking advantage of the nuns "fragile financial condition", "the transaction should be declared void as a product of elder abuse.
"It appears that it was ideal for Hollister, but terrible for the sisters."
The nuns lawyer Bernard Resser said, speaking outside court: "Ultimately, for any sale, the Pope has to approve - for Katy Perry or anyone else."
In a statement their legal team added: "The Sisters of the Immaculate Heart of Mary have shown great courage in maintaining their independence and have demonstrated they are self-sufficient and capable of conducting their own affairs.
"We think today's hearing and the comments the judge made during the hearing indicate that he clearly understood the Sisters' concern about their security and welfare."
