In 1988, Pope John Paul II announced that Fellay and three others were automatically excommunicated for being consecrated as bishops by Archbishop Marcel Lefebvre, an act that the Holy See described as "unlawful" and "schismatic".

On 17 June 1988 Cardinal Bernardin Gantin, prefect of the Congregation for Bishops sent the four priests a formal canonical warning that he would automatically incur the penalty of excommunication if they were to be consecrated by Lefebvre without papal permission.

On 1 July 1988, Cardinal Gantin issued a declaration stating that Lefebvre, de Castro Mayer, Fellay, and the three other newly ordained bishops "have incurred ipso facto the excommunication latae sententiae reserved to the Apostolic See".

[4] Cardinal Darío Castrillón Hoyos, head of the commission responsible for implementing Ecclesia Dei, has said this resulted in a "situation of separation, even if it was not a formal schism.

Florian Abrahamowicz, a SSPX's dean of Northeastern Italy, called the action "insulting," since it claimed to remit an excommunication of these four bishops that the Society had officially maintained since 1988 did not exist.

[12] Cardinal Antonio Cañizares Llovera, Prefect of the Congregation for Divine Worship and the Discipline of the Sacraments, has reported Fellay as declaring that if Archbishop Lefebvre had seen how Mass is celebrated in an abbey near Florence in strict accordance with the 1970 Missal, he would not have taken the step that he did take.

In addition to disputes over the changes introduced by the Second Vatican Council, new problems have been created by plans for the beatification of Pope John Paul II.

[15] However, on 12 October 2013, Fellay declared, "We thank God, we have been preserved from any kind of agreement from last year", saying that the society had withdrawn the compromise text that it presented to Rome on 15 April 2012.

[16] On the same occasion, he spoke of the Third Secret of Fatima as seemingly foretelling "both a material chastisement and a great crisis in the Church" and described Pope Francis as "a genuine Modernist", who, in late July 2013, had begun a series of contacts, regarding which Fellay said: "We may not have the entire picture at this point, we have enough to be scared to death.

"[17] On 28 December 2012, in a radio interview aired from Our Lady of Mount Carmel Chapel in New Hamburg, Ontario, Canada, Bishop Fellay declared, "Who, during that time, was the most opposed that the Church would recognize the Society?

"[19] On 9 December 2014, Bishop Fellay came at the European Parliament of Brussels and blessed the nativity scene made by the artisan masters of San Gregorio Armeno, Naples, on an initiative of the Italian politician Mario Borghezio (Lega Nord) and at the presence of the Veneto's governor Luca Zaia.

The twenty-five page document, which was made public in September after receiving no reply from the Holy See, stated that the Pope could possibly be saying various words, actions and omissions during his pontificate going against charity and the Church.