The Roman Catholic Church in Poland was in turmoil on Monday as a second prelate stepped down because of his Communist-era secret police ties, after Sunday’s resignation of this city’s archbishop over similar allegations.

Questions spread about just how broad and deep a stain secret-police collaboration has left on a church long regarded as a beacon of faith and freedom during the Communist era. Many people also have asked how or why the Vatican could have invited the storm by appointing a man to such a sensitive post despite knowing that he had a clouded past.

“The people responsible for the procedure of appointing such candidates applied the traditional way of doing it, which means it was without an investigation and was based on their confidence in the truthfulness of the candidate,” said the Rev. Dariusz Kowalczyk, head of the Jesuits in Warsaw.

In short, church officials from Warsaw to Rome suggested that the archbishop, Stanislaw Wielgus, alone was to blame.

But many people here worry that a mishandling of the affair could permanently damage the last major bastion of Roman Catholic faithful in Europe at a time when the Polish church is already facing the secularizing trend that has emptied churches in Italy, France and Spain.