The Vatican has finally acceded to demands for a formal inquiry into Britain's most senior Catholic cleric, Cardinal Keith O'Brien, who resigned from the diocese of St Andrews and Edinburgh in February following allegations of sexual misconduct.

An apostolic visitation, a high-level inspection in which the "visitator" is given authority directly by the pope, will take place in the diocese, which has been accused of having had a "gay mafia" during the cardinal's tenure.

News of the apostolic visitation came via the papal nuncio, Antonio Mennini, in a meeting with one of the complainants, a former priest known as "Lenny" who accused the cardinal of making sexual advances to him when he was a seminarian. "The archbishop told me the holy see had decided there would be an investigation into all of the allegations. Anyone affected would be able to give evidence. If it is judged that there is sufficient evidence, then it would go to another, deeper process in Rome," said Lenny.

Lenny expressed relief that the facts would finally be examined.

"I am glad the Catholic church has faced up to the need for a process to determine the truth," he said. "If this story had not gone public in the Observer in February, if there had not been consistent calls for action, we would not have got to this point. But it's now important to scrutinise the scope and remit of the visitation.

"It must address Keith O'Brien's behaviour, but also examine whether any promotions were awarded to the cardinal's cronies."

However, Lenny was dismayed by the nuncio's insistence that the visitator should be the new archbishop of St Andrews and Edinburgh. O'Brien's successor is expected to be announced this month and there is widespread speculation that he will be a Scot currently working in Rome.

"I told Archbishop Mennini that the process was not likely to reach the truth if it was conducted by the new archbishop, whoever that turns out to be. Priests are hardly likely to be completely frank with someone who holds their lives in his hands for years to come. I hope the nuncio rethinks."

"It would be ridiculous to appoint the cardinal's successor," agreed Tom Doyle, a senior canon lawyer who worked at the nunciature in Washington before representing abuse victims all over the world in cases against the Catholic church.

"The whole point is that it's someone from outside. If they appoint O'Brien's successor to lead the investigation, they are going to look like fools."

The cardinal's resignation and removal from Scotland for six months of prayer and penance had cast doubt over an inquiry.

In a statement in March, he acknowledged: "My sexual conduct has fallen below the standards expected of me as a priest, archbishop and cardinal." The admission suggested that his behaviour had covered a long period, but because it was non-specific the allegations have subsequently been minimised.

Mennini's only public pronouncement has been that the cardinal made mistakes but had also done "a lot of good". "He didn't say anything about Keith's victims," said Lenny. "I told him that was deeply offensive and hurtful."

"It's blame-shifting," said Doyle. "Hitler created the autobahn and Mussolini made the trains run on time. That's not the point.

"Probably good was done while O'Brien was in charge, but the fact is that people's lives were seriously, seriously harmed by him. That's certain."

Senior figures in Rome say the apostolic visitation is a way of dealing not just with the cardinal but with the more general accusations of moral malaise sweeping the church in Scotland.

"Given that the Cardinal O'Brien case seems to be a salient feature of a larger network of dysfunction, an apostolic visitation could be a very appropriate way of addressing the larger problem," said Father Robert Gahl, an associate professor of ethics at the Pontifical University of the Holy Cross in Rome.

Doyle, who was involved in several apostolic visitations in Washington, is less convinced. Ireland's apostolic visitation in 2011, following widespread child abuse cases, was a "total farce", he said.

"I don't think an apostolic visitation will achieve much. In my experience of sexual abuse – which dates back 30 years – the only significant truth that has ever arisen has been when totally independent investigations have been carried out.

"In America, it's been grand juries. In Ireland, it's been statutory commissions. If they are really looking into alleged abuse by Keith O'Brien, the only way to do it is to appoint outside investigators who have free rein. But they won't."