A letter addressed to the papal nuncio, Archbishop Charles Brown, was handed in by the Irish branch of the We Are Church lay movement.
The protesters were mainly in their 60s or older, and two-thirds of them were women. They carried a banner that read "Dialogue Yes. Silence No." and sang the 1960s protest song of the civil rights movement, "We Shall Overcome."
The letter stated that the Vatican Congregation for the Doctrine of the Faith had acted unjustly in its treatment of Flannery and should now restore him to his full priestly ministry.
"Catholics have to be grateful for the courage of Fr. Flannery in exposing the unacceptable insidious methods used by the congregation in silencing priests like Tony and many others," said Brendan Butler, the organizer of the protest, who also announced that a petition calling on the doctrinal congregation to restore Flannery to the ministry had by Sunday evening been signed by 1,400 Catholics in Ireland and from all over the world.
However, Brown was not at the residence, having traveled to County Cork for the consecration in Cobh Cathedral of Kerry priest William Crean as the 67th bishop of Cloyne and Ross in succession to the former secretary to three popes, John Magee.
Meanwhile, controversy continued over reported quotes from "senior Vatican sources" denying Flannery's claims that he was threatened excommunication by the congregation.
But documents seen by the Sunday Independent in Dublin appeared to vindicate Flannery's assertion.
Following Flannery's coming under investigation a year ago for his writings in the Redemptorist magazine, the correspondence shows that the doctrinal congregation complained that he expressed heretical or heterodox views and pointed out that "a priest who has committed the delict [act] of heresy" incurs a "latae sententiae [automatic] excommunication."
Among demands made by the doctrinal congregation were for Flannery to accept that "ordination of women is not possible," but he said he still believes in ordaining women priests.
Butler told NCR that his group is considering traveling to Rome for delivery of the signatures to the Congregation for the Doctrine of the Faith prefect Archbishop Gerhard Müller.