The Australian cardinal appointed by the Pope to control the Vatican’s finances — the Roman Catholic Church’s third highest post — will face trial on sexual abuse charges.

Cardinal George Pell, 76, a former Oxford and Cambridge scholar, took leave from the Vatican last year to defend himself. He appeared in a packed Melbourne courtroom this morning to hear a magistrate rule that there was enough evidence to commit him to trial.

In a decision that will rock the Vatican and the Catholic Church’s leadership around the world, Belinda Wallington, the magistrate, rejected strenuous earlier efforts by the cardinal’s legal team to have all the charges thrown out.

Cardinal Pell did not change expression, apart from a brief glance at the overflowing court’s floor. The 6ft 3in clergyman, a former college Australian Rules football star known as Big George, brought his hand to his mouth and coughed.

He is to stand trial on charges of alleged sexual offending in the 1970s, when he was still a priest. Later alleged sexual abuse offences are said to have occured in the 1990s when he was archbishop of Melbourne.

The first offences are alleged to have occurred when he was a priest in the Catholic diocese of Ballarat, a city 70 miles west of Melbourne that a royal commission described last year as having suffered a “catastrophic failure of leadership” in dealing with allegations of child sexual abuse by clergy. Later alleged incidents are said to have taken place in Melbourne.

The magistrate asked the cardinal how he would plead after issuing the formal advice that a judge would take into consideration a guilty plea during sentencing.

“Not guilty,” Cardinal Pell said in a booming voice.

Ms Wallington took more than an hour to read her decision. Her first ruling struck out the most serious allegations against him. The allegations dated to 1978 and 1979 in Ballarat; one complainant has died since the charges were laid by police and another was found medically unfit to give evidence. The magistrate also cited inconsistencies in the evidence of one complainant.

The full details of the remaining allegations have yet to be released to the public, though they are understood to date back decades.

The cardinal’s legal team, headed by Robert Richter, QC, had argued to have all charges thrown out, saying that the allegations were “impossible”, the product of “fantasy, mental health problems or pure invention” and that Cardinal Pell’s accusers were motivated by a desire to punish the Catholic Church.

Cardinal Pell had arrived at the court in a white sedan just after 9am. He was escorted to the door by up to 40 police officers, who separated his path from the public. Protesters carried with laminated signs reading: “Every child deserves a safe and happy childhood.”

The former archbishop of Sydney was appointed by Pope John Paul in 2014 as the inaugural prefect of the secretariat for the economy, the Vatican’s third highest post. He was tasked with reforming the Vatican’s finances and within a year had brought out a new financial handbook for the church which, he said, would bring transparency and international standards to Vatican accounting.

For Cardinal Pell the charges are a threat to his freedom, his reputation and his gilded career. For Pope Francis they are a challenge to his credibility in the light of his promise of a “zero tolerance” policy for sex abuse in the church.

Pope Francis has withheld judgment of Cardinal Pell, saying that he wants to wait for justice to run its course. He did not force him to resign; Cardinal Pell took immediate leave of absence last June so that he could return to Australia to fight the charges. He has said that he intends to return to the Vatican and to his high office once the case is resolved.