The Catholic Church in Scotland is facing its gravest crisis since the Reformation, according to a Scots historian.

Professor Tom Devine’s comments follow the resignation of Cardinal Keith O’Brien, who stood down from his post following allegations of ‘inappropriate behaviour.

The 74-year-old has denied the allegations.

Professor Devine, a personal senior research professor of history in the University of Edinburgh, said: “This is probably the gravest single public crisis to hit the Catholic Church in Scotland since the Reformation and its effects in the short term are incalculable. Many of the faithful in Scotland will be stunned by the seismic turn of events and left demoralised.”

However, the senior Edinburgh University research professor said that the powerful resilience of global faith and the church should not be underestimated.

In full: professor Tom Devine’s reaction to Cardinal O’Brien’s resignation

Cardinal O’Brien announced his resignation yesterday in the face of allegations of inappropriate behaviour towards young priests.

He had been due to formally submit his resignation in three weeks, but stood down with immediate effect after weekend revelations he was being investigated for the claims, which date back 30 years and relate to three priests and a former priest.

The 74-year-old will also not attend the conclave to choose the successor to Pope Benedict, who steps down on Thursday, a move that leaves the Catholic Church in the UK with no vote in the election.

Cardinal O'Brien, whose resignation had to be accepted by the Pope, said: "The Holy Father has now decided that my resignation will take effect today.

"I do not wish media attention in Rome to be focused on me – but rather on Pope Benedict XVI and on his successor."

The Cardinal had denied the allegations on Sunday, when he also said he was taking legal advice.

He added yesterday: "Looking back over my years of ministry: For any good I have been able to do, I thank God. For any failures, I apologise to all whom I have offended."

Meanwhile, it emerged he was previously at the centre of a row over the cover-up of evidence that a priest had sexually abused teenage boys.

As Archbishop in the early 1990s, Cardinal O'Brien arranged £42,000 compensation for one of the victims of Father Desmond Lynagh. Police were not originally informed but he was later jailed for three years in 1996.

Lynagh, 55, had admitted shameless and indecent conduct towards two youths in the mid-1970s, while teaching at the Church's then Scottish national training college, Blairs College, near Aberdeen.

One leading authority on the Church described "the gravest single public crisis to hit the Catholic Church in Scotland since the Reformation", while other influential members of the Catholic laity have said the shock timing of the resignation should provide an opportunity to change the autocratic culture of the Church north of the Border.

It is unclear whether the Vatican will appoint another cardinal to Scotland in the short to medium term, while cardinal O'Brien's earlier-than-expected resignation leaves half of all Scottish dioceses requiring a bishop.

The resignation will be a major credibility blow to the Church's high-profile crusade against same-sex marriage.

Kelvin Holdsworth, the Provost of St Mary's Cathedral, Glasgow, addressing the allegations facing the cardinal, said "such talk has been doing the rounds privately for some time".

Leading historian Professor Tom Devine claimed that, "in the interests of fairness it is now time for O'Brien's anonymous accusers to step forward into the public domain".

Lothian and Borders Police said they had received no complaints about the claims, which the cardinal continues to contest.

It was reported that three priests and a former priest at the centre of the allegations in the St Andrews and Edinburgh Archdiocese submitted four statements to the Papal Nuncio Antonio Mennini's office the week before Pope Benedict's resignation was announced on February 11.

The statements, it is alleged, detailed inappropriate advances and "unwanted behaviour" by the cardinal in the 1980s, on one occasion after late-night drinking.

Before the development, cardinal O'Brien had been due to formally apply to resign when he turns 75 on March 17, and, because of mounting health problems, he was expected to be allowed to retire. It is unlikely he would have stood down until the summer.

But in its statement, the Scottish Catholic Media Office said: "The Holy Father Pope Benedict XVI has accepted

on February 18, 2013 the resignation of His Eminence Cardinal Keith Patrick O'Brien from the pastoral governance of the Archdiocese of Saint Andrews and Edinburgh. This information will be announced and published in the Osservatore Romano of Monday February 25, 2013."

Reacting to the acceptance of his resignation, Cardinal O'Brien said: "Approaching the age of 75 and at times in indifferent health, I tendered my resignation as Archbishop of Saint Andrews and Edinburgh to Pope Benedict XVI some months ago.

"I was happy to know that he accepted my resignation 'nunc pro tunc' (now, but to take effect later) on November 13, 2012.

"The Holy Father has now decided that my resignation will take effect today, February 25, 2013, and that he will appoint an Apostolic Administrator to govern the Archdiocese in my place until my successor as Archbishop is appointed.

"I have valued the opportunity of serving the people of Scotland and overseas in various ways since becoming a priest.

"Looking back over my years of ministry: For any good I have been able to do, I thank God. For any failures, I apologise to all whom I have offended.

"I thank Pope Benedict XVI for his kindness and courtesy to me and on my own behalf and on behalf of the people of Scotland, I wish him a long and happy retirement.

"I also ask God's blessing on my brother cardinals who will soon gather in Rome to elect his successor. I will not join them for this conclave in person."

The cardinal remained in his residence at Morningside in Edinburgh after the announcement.

One of his visitors was Monsignor Thomas Chambers, who was with the cardinal as the announcement that the Pope had accepted his resignation was made.

As he drove out, the Right Rev Mgr Chambers told waiting journalists: "I have seen him and he's doing fine."

Asked how the Church would come through this latest crisis, he said: "It's over 2000 years old – it's survived a lot. So we'll come through this together."