It is likewise the Plenary Assembly which elects the members of the Permanent Council, the Chairmen of the Episcopal Commissions and the heads of the agencies attached to the Conference.

The Permanent Council, composed of ten elected members representing the Luzon, Visayas and Mindanao regions, acts in accordance with the Constitution and By-Laws of the CBCP, and the policies and standing decisions of the Plenary Assembly.

The Permanent Council's regular functions include ensuring that the decisions made during the Plenary Assembly are properly executed and directing the activities of the Office and other agencies of the Conference.

[8] A crucial function of the Permanent Council is to prepare the Joint Statements or Pastoral Letters of the Hierarchy on subject matters decided on by the Plenary Assembly, and see to it that copies are sent to the members for comment and/or approval before they are officially released.

[8] The council is likewise mandated to work with the Episcopal Commissions and assign to them functions of urgent character which may not have been taken up in the Plenary Assembly and which may not be provided for in the Constitution.

The episcopal conference expressed dismay (July 6, 2007) over the conduct of the May 14, 2007, midterm elections, saying "the challenge of credible, honest, meaningful and peaceful polls remains".

[10] The CBCP, in a press conference, further called for a change of leadership at the Commission on Elections as it noted the "continuing dominance" of political dynasties, dagdag-bawas, and poll violence.

Demanding "full revamp of the Comelec", it sought for the appointment of people with "unquestioned integrity and competence, especially in systems and management" to succeed Chair Abalos and the five other members.

[12] On December 17, 2007, in a statement on the Catholic Bishops Conference of the Philippines (CBCP) website, Pampanga archbishop Paciano Aniceto stated that Pope Benedict XVI assured Filipinos that God and the church are still with them – in his encyclical "Spe Salvi facti sumus (In hope we are saved).

Three priests—Crisanto de la Cruz, Ronilo Maat Omanio and Ed Panlilio—who ran in the last elections were suspended from their pastoral duties as a result of their entry into the political arena.

[14] On January 19, 2008, the Catholic Bishops Conference of the Philippines (quoting from a letter of Vatican Cardinal Secretary of State Tarcisio Bertone) announced that Pope Benedict XVI "praised the courage of, and was saddened over the brutal and tragic killing of Reynaldo Roda in his ministry as head of Notre Dame School."

The Pope wrote Jolo Bishop Angelito Lampon: "calls upon the perpetrators to renounce the ways of violence and to play their part in building a just and peaceful society, where all can live together in harmony.

[27] The CBCP was embroiled in a controversy in 2011 over millions of pesos in donations from the Philippine Charity Sweepstakes Office at the behest of then president Gloria Macapagal Arroyo.

[29] Shay Cullen, founder of the People's Recovery Empowerment Development Assistance Foundation, accused CBCP members of covering up cases of sexual abuse and misconduct.

[42][43] The John Mary Vianney Galilee Development and Retreat Center for Priests, a 54-room institution would be inaugurated on August 15, 2007 by Manila Archbishop Cardinal Gaudencio Rosales.