The crisis engulfing the Catholic Church deepened tonight as the outgoing Pope effectively sacked Britain's most senior cleric, following allegations of inappropriate behaviour towards young priests.

Cardinal Keith O'Brien apologised to "all whom I have offended", but his immediate removal from office means that he will not now travel to Rome to choose a successor to Pope Benedict XVI - an attempt by the Vatican to prevent the occasion being overshadowed by further scandal.

The Vatican faces mounting pressure also to ban other cardinal electors tainted by allegations of sexual impropriety.

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Cardinal Keith O'Brien is the first Catholic clergyman of the highest rank to be forced out since Cardinal Groer in 1998, when the Austrian apologised but did not admit molesting youths at a monastery in the 1970s.

It was alleged that attempts by the then Cardinal Joseph Ratzinger to investigate were blocked by Pope John Paul II. The Vatican faces demands to exclude other cardinal electors tainted by allegations of sexual impropriety from attending the conclave, which could now start as early as this week after the Pope again defied convention by scrapping the 15-day waiting period between pontiffs.

The resignation of Archbishop O'Brien was welcomed by gay-rights campaigners who have been enraged at the 74-year-old clergyman's strident opposition to same-sex marriage.

The Archbishop of Edinburgh is the leader of Scotland's Roman Catholics and Britain's only cardinal elector. His decision to stand down means the UK will have no say in the choice of the next leader of the world's 1.2 billion Roman Catholics. In his resignation statement the Cardinal apologised "to all whom I have offended". Although he has not spoken publicly on the issue it is understood that he continues to contest allegations from the 1980s that he made unwanted advances towards four members of the clergy, including three current priests.

An investigation is underway into the claims, which resulted in one of the men requiring long-term psychological counselling.

Archbishop O'Brien said the Pope had initially accepted his resignation in November last year but it was due to take effect to coincide with his 75th birthday in March. Cardinals under the age of 80 are still entitled to attend the conclave to vote. However, following weekend newspaper revelations, he said: "The Holy Father has now decided that my resignation will take effect today and that he will appoint an apostolic administrator to govern the Archdiocese in my place until my successor as Archbishop is appointed. I do not wish media attention in Rome to be focused on me – but rather on Pope Benedict XVI and on his successor."

Some welcomed the resignation of the man who, despite recently calling for clergy to be allowed to marry, has built a hardline reputation fighting against abortion and gay rights. Ben Summerskill, chief executive of the charity Stonewall, which awarded the Cardinal the title "bigot of the year", called for a full investigation into the claims against him.

"We hope that his successor will show a little more Christian charity towards openly gay people than the Cardinal did himself," Mr Sumerskill said.

Catherine Pepinster, editor of The Tablet, said the resignation was "devastating for Catholics", adding: "If he had attended the discussions that are about to begin in Rome about the election of a new Pope, it could have been a circus, so it's right that he isn't going."

With the Pope due to become the first in 600 years to stand down on Thursday, the Vatican has been forced to repeatedly deny rumours that the scandal over sex abuse was about to engulf the Pontiff himself.