Britain’s former most senior Catholic blocked an independent inquiry into cases of clerical sexual abuse covering 60 years before he resigned after making homosexual advances to other priests, officials said today.

The Bishops’ Conference of Scotland in 2011 commissioned a report into allegations of abuse but it was halted the following year when its then head, Cardinal Keith O’Brien, withdrew his support. A spokesman for the Catholic Church said that a “national audit” was not possible without the support of the Cardinal and the analysis was stopped.

The Cardinal stepped down as Archbishop of St Andrews and Edinburgh in February after current and former priests made allegations of inappropriate behaviour against him.

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The intervention of Cardinal O’Brien was revealed in a letter to the Catholic newspaper The Tablet by the retired Archbishop of Glasgow, Dr Mario Conti. He said the intention of the Bishops was to publish the results of the audit, but its scope was not clear. A police investigation is under way into allegations of historic sexual abuse at two Catholic boarding schools in the Scottish Highlands. More than 20 people have come forward to say they were victims of physical and sexual abuse by a number of Benedictine monks who ran the Fort Augustus Abbey school and Carlekemp, its feeder school in East Lothian, from the 1950s to the 1990s. Both schools are now closed.

One of Scotland’s most senior Catholics, the Bishop of Aberdeen Right Reverend Hugh Gilbert, apologised to former pupils during mass at Fort Augustus church earlier this month.

He said: “It is a most bitter, shaming and distressing thing that in this former Abbey school a small number of baptised, consecrated and ordained Christian men physically or sexually abused those in their care. All that can be done should be done for the victims.”

Following his resignation, Cardinal O’Brien, 75, stated that he would play no further part in the public life of the Catholic Church in Scotland and has since left the country for a period of “spiritual renewal and reflection”.