On May 28, 1948, Pope Pius XII appointed him Secretary to the Commission for Liturgical Reform. This body was responsible for the reform of the rites for the Easter Vigil (1951) and then for the whole of Holy Week (1955). It went on to reform the Code of Rubrics (1960) which affected both the Mass and the Divine Office before producing new editions of the Roman Breviary in 1961 and the Roman Missal in 1962.
Fr. Bugnini had been secretary of the Council's Preparatory Commission for the Liturgy. The Council - for which Fr Bugnini was appointed as a peritus - voted in the new Constitution on the Sacred Liturgy, December 4, 1963. On January 3, 1964, Pope Paul VI appointed Bugnini as Secretary of the Consilium for the Implementation of the Constitution on the Liturgy ("the Consilium" for short).
On January 4, 1976, the Vatican announced Bugnini's appointment as Pro-Nuncio to Iran. There, not only did he deal with the ordinary business of a papal nunciature, but he also studied and acquired knowledge of the country, its history, and its cultural, religious, and social traditions. The result was his book La Chiesa in Iran ("The Church in Iran"). Once he completed that book, he wrote the well-known resource, "The Reform of the Liturgy 1948-1975."
As Papal Representative to Iran, Bugnini tried in 1979 to obtain, in the name of the pope, the release of the American hostages. The elderly Nuncio met with Ayatollah Ruhollah Khomeini, the Iranian leader, to deliver Pope John Paul II's appeal for the release of the hostages, but the Ayatollah rejected the appeal. The 52 Americans were eventually released on January 21, 1981, after 444 days in captivity.
In many circles, particularly in the traditionalist Catholic community, believe that Bugnini was a Freemason, a serious accusation against any Catholic, especially a senior prelate. Some claim that this was why he was suddenly transferred from his Roman Curia job to a quite different posting in the Holy See's diplomatic service, and that it explains what they regard as the excessively modernistic course of the liturgical reform. The allegation remains fiercely disputed, and has never been conclusively proven.
While Bugnini was still working as Secretary of the Consilium, rumours started to appear in the Italian press that he was a Freemason. Bugnini reported in his memoirs that a conservative cardinal told him in summer 1975 that a "dossier" showing him to be a Freemason had been brought to the Pope's desk. The conservative Vatican prelate Cardinal Silvio Oddi is reported to have commented "I can swear that he was not a Freemason.... I remain convinced that these accusations were made up by someone in his office... who wanted to eliminate him".
The Vatican made no immediate denial of either the April 1976 rumours concerning the grounds for his dismissal or of the reports in June 1976 that not only Bugnini, but over 100 other Vatican officials (including cardinals) were Masons; but it later issued a blanket denial on L'Osservatore Romano of October 10, 1976: "Not one, we say, not one of the accused Vatican prelates has ever had anything to do with Freemasonry. We say this in order to rebut the possible accusation that silence signifies consent.
The English Traditionalist Roman Catholic writer Michael Davies investigated the allegations, and claimed to have made contact with a priest who "came into possession of what he considered to be evidence proving Mgr Bugnini to be a Mason" and who had "this information placed in the hands of Pope Paul VI by a cardinal". The Australian seminary professor Fr. Brian Harrison, while discounting the views of Davies, said that he too had heard, second hand, of a Roman priest who found evidence against Bugnini in a briefcase he left behind in a conference room.