In an eight-page letter, the pontiff rebuked the American clergy and said the sex abuse scandal had caused a "crisis of credibility" for the Church that's been made worse by cover-ups.
The letter was released by the Vatican and delivered to US bishops attending a retreat in Chicago.
He also criticised division among the bishops and called on them to show unity and address the issues in light of the Gospel.
"God's faithful people and the Church's mission continue to suffer greatly as a result of abuses of power and conscience and sexual abuse, and the poor way that they were handled," he wrote.
He said the bishops had "concentrated more on pointing fingers than on seeking paths of reconciliation".
A grand jury report in Pennsylvania made public last year documented how paedophile priests were often protected by church hierarchy or moved to other postings without the faithful being told of the priests' sexual predatory history.
More than 1,000 victims were abused by hundreds of priests over seven decades in Pennsylvania alone.
Pope Francis has requested senior Catholic bishops from around the world visit the Vatican next month to discuss the best way to protect minors in their care.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.