The Tuesday's apology followed a string of child abuse scandals to hit the Catholic Church, including in Ireland, the United States, Germany and Malta.
"We want to seek pardon from those who have been victims of abuse by dishonest priests who have damaged innocent children with their abominable actions," said a statement from the Mexican Bishop's Conference at their annual meeting.
They also promised to allow civil authorities to intervene to apply the law in church-linked sex abuse cases.
The apology followed another last month from Mexico's Legion of Christ religious order -- which is present in 22 countries -- for the "reprehensible actions" of their late founder Marcial Maciel.
Longstanding allegations against Maciel finally led Pope Benedict XVI to bar him from active duty in 2006, two years before he died aged 87.
Benedict has recently faced allegations that he failed to take action against predator priests both as head of the Vatican's top doctrinal and morals enforcer and earlier as the Munich archbishop.
The Vatican on Monday stepped up its defense of action taken over abuse scandals, releasing new guidelines which state that accused priests should be handed over to civil authorities.
The Mexican church defended Benedict for the "bravery with which he has expressed himself" on pedophilia cases.
"There are many virulent and unfair attacks" against the pope, the statement said.
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SIC: AFP