The head of the Catholic church in Phoenix has stripped Arizona's largest hospital of its Catholic affiliation after he ruled that a decision to save the life of a mother by terminating her 11-week pregnancy was morally wrong.

Bishop Thomas Olmsted announced yesterday that St Joseph's hospital can no longer be considered to be Catholic. The ruling breaks a relationship that stretches back to the hospital's founding by Catholic nuns 115 years ago.

He has also excommunicated the member of the hospital's ethics committee that permitted the abortion to go ahead.

The schism brings to a head a dispute that has been building for several months over the termination, performed in November 2009, at St Joseph's hospital and medical centre.

The case concerned an unidentified woman in her 20s, who had a history of abnormally high blood pressure that was under control before she became pregnant. But doctors were concerned on learning of the pregnancy about the extra burden that would be placed on her heart, and they monitored her closely.

Tests showed that in the early stages of pregnancy her condition deteriorated rapidly and that before long her pulmonary hypertension – which can impair the working of the heart and lungs – had begun to seriously threaten her life. Doctors informed her that the risk of death was close to 100% if she continued with the pregnancy.

Consultations were then held with the patient, her family, her doctors and the hospital's ethics team, and the decision to go ahead with an abortion was taken in order to save the mother's life.

The hospital's president, Linda Hunt, said following the bishop's severing of relations that the operation had been "consistent with our values of dignity and justice. If we are presented with a situation in which a pregnancy threatens a woman's life, our first priority is to save both patients. If that is not possible we will always save the life we can save, and that is what we did in this case."

But Olmsted did not see it that way. He drew on the advice of the US Conference of Catholic Bishops' doctrinal committee, which distinguishes between direct abortions that are never justifiable and indirect terminations that happen incidentally as a result of life-saving medical procedures that can be allowed on narrowly-defined grounds.

In this case, the operation was deemed to be a direct abortion because the pregnancy was ended to ease the mother's separate health problem.

"The baby was healthy and there was no problems with the pregnancy; rather, the mother had a disease that needed to be treated. But instead of treating the disease, St Joseph's decided that the healthy, 11-week-old baby should be directly killed. This is contrary to the teaching of the church," Olmsted said.

St Joseph's has 697 beds and 5,000 staff, and this year admitted 40,000 in-patients. It is world-renowned for its work on Parkinson's disease and neurosurgery, and is regularly voted among the top 10 hospitals in the US.

Hunt said that the hospital was "deeply saddened" by the church's decision but that "we will be steadfast in fulfilling our mission". In a statement, St Joseph's said it would perform the same treatment again were the life of a mother in danger.

It is not known how the church hierarchy found out about the termination, as the hospital abides by a strict privacy policy for all patients.

The split will not affect the hospital's income as the church does not fund it. The only visible change that will be evident immediately is that the blessed sacrament will be removed from the hospital's chapel and mass will no longer be held there.

But the name of St Joseph's will remain, and the management has vowed that the institution's Catholic heritage will still be at its core.