The Vatican refused to allow its officials to testify before an Irish commission investigating the clerical abuse of children and was angered when they were summoned from Rome, US embassy cables released by WikiLeaks reveal.

Requests for information from the 2009 Murphy commission into sexual and physical abuse by clergy "offended many in the Vatican" who felt that the Irish government had "failed to respect and protect Vatican sovereignty during the investigations", a cable says.

Despite the lack of co-operation from the Vatican, the commission was able to substantiate many of the claims and concluded that some bishops had tried to cover up abuse, putting the interests of the Catholic church ahead of those of the victims. Its report identified 320 people who complained of child sexual abuse between 1975 and 2004 in the Dublin archdiocese.

A cable entitled "Sex abuse scandal strains Irish-Vatican relations, shakes up Irish church, and poses challenges for the Holy See" claimed that Vatican officials also believed Irish opposition politicians were "making political hay" from the situation by publicly urging the government to demand a reply from the Vatican.

Ultimately, the Vatican secretary of state, Cardinal Tarcisio Bertone (equivalent to a prime minister), wrote to the Irish embassy, ordering that any requests related to the investigation must come through diplomatic channels.

In the cable Noel Fahey, the Irish ambassador to the Holy See, told the US diplomat Julieta Valls Noyes that the Irish clergy sex abuse scandal was the most difficult crisis he had ever managed.

The Irish government wanted "to be seen as co-operating with the investigation" because its own education department was implicated, but politicians were reluctant to press Vatican officials to answer the investigators' queries.

According to Fahey's deputy, Helena Keleher, the government acceded to Vatican pressure and granted them immunity from testifying. Officials understood that "foreign ambassadors are not required or expected to appear before national commissions", but Keleher's opinion was that by ignoring the commission's requests the clergy had made the situation worse.

The cable reveals the behind-the-scenes diplomacy in which politicians in the Irish government attempted to persuade an imperious Vatican to engage with the investigation.

The foreign minister, Michael Martin, "was forced to call in the papal nuncio (representative)" to discuss the situation. The ambassador reported that resentment towards the church in Rome remained very high in Ireland, largely because of the institutionalised cover-up of abuse by the Catholic church hierarchy.

Finally the Vatican changed tactics and on 11 December 2009 the ambassador stated that the pope had held a meeting with senior Irish clerics. The Irish cardinal Seán Brady and the archbishop of Dublin, Diarmuid Martin, went to Rome and met the pontiff, who was flanked by Bertone and four other cardinals.

At the end of the meeting, the Vatican issued a statement saying that the pope shared the "outrage, betrayal, and shame" of Irish Catholics, that he was praying for the victims, and that the church would take steps to prevent recurrences.

On 21 March this year, Benedict issued a letter savaging the Irish bishops for their earlier handling of the crisis: "Grave errors of judgment were made and failures of leadership occurred. All this has seriously undermined your credibility and effectiveness."

He also apologised to the victims: "You have suffered grievously and I am truly sorry. I know that nothing can undo the wrong you have endured. Your trust has been betrayed and your dignity has been violated. It is understandable that you find it hard to forgive or be reconciled with the church. In her name, I openly express the shame and remorse that we all feel."

In a section entitled "Some Lessons Learned, but Crisis Will Play Out for Years", the ambassador related that his contacts at the Vatican and in Ireland expected the crisis in the Irish Catholic church to be protracted over several years, as the Murphy commission dealt only with allegations from the Dublin archdiocese.

They believed further investigations into other archdioceses would lead, "officials in both states lament, to additional painful revelations".