Cardinal Reinhard Marx said he was ashamed over the decades of abuse that have shattered trust, the crimes carried out by officials of the Church, as well as how so many have looked away for so long.
The dismay expressed by the head of the German Bishops' Conference came as the institution published a damning report showing that in Germany, almost 3,700 minors - mostly boys - were assaulted between 1946 and 2014.
The report's authors said however that the figure was "the tip of the iceberg" and that the real extent of the problem was far greater.
"I have to say very clearly that sexual abuse is a crime. Those who are guilty must be punished," said Cardinal Marx.
"For all the failures and for all the pain, as chairman of Germany's Bishops Conference, I apologize. I also apologize on a personal basis.
"We are not done with confronting the incidents and consequences, it begins
now," he stressed at a press conference.
Predator priests
According to the study, 1,670 clergymen in Germany committed some form of sexual attack against 3,677 minors, mostly boys, between 1946 and 2014, intimidating their victims into keeping quiet.
More than half of the victims were 13 years old or younger, the study concluded, after examining 38,000 documents from the 27 German dioceses.
The survey's researchers warned that the true scale of the abuse was far greater, as many documents had been "destroyed or manipulated".
Predator priests were often transferred to another parish, which was not warned about their criminal history. Only about one in three were subject to disciplinary hearings by the
Church, and most got away with minimal punishment. Only 38 percent were prosecuted by civil courts.
'Abuse, transfers, cover-ups'
Victims have criticised the report for falling short of what is needed to flush out perpetrators.
They urged the Church to bring in independent experts for a thorough audit and called for victim compensation.
"The system of abuse, transfers (of offending priests) and cover-ups cannot be mapped out" by a study that had access only to available personnel documents, said the victims' association Eckiger Tisch.
"There are no names given of the responsible bishops who have perfected the system of covering up sexual attacks over decades."
Justice Minister Katarina Barley also urged the Church to work with state prosecutors to bring every known case to justice.
Cardinal Marx acknowledged that a thorough reckoning of the problem was "absolutely necessary" but underlined that the process was colossal and would require time.
"We can't just publish names. A complete rehabilitation also includes dialogue. Maybe a truth commission," he said, promising action.
'Shocking and probably the tip of the iceberg'
Barley said the study was "shocking and probably just the tip of the iceberg". She urged the Church to "take responsibility for decades of concealment, cover-ups and denials"..
The independent commissioner for child sex abuse issues, Johannes-Wilhelm Rörig, recommended state authorities step in to clear up the crimes and ensure victims get access to Church files and compensation.
The state "has a duty of care for all children, including those who are in the care of the Church", he had told the Süddeutsche newspaper.
A victims support hotline and a dedicated website with information will be put in place during the meeting.
Systemic abuse
The Catholic Church has since the 1980s been battered by scandals of rape, sexual abuse, paedophilia and physical abuse.
Pope Francis has found himself embroiled after conservative US Archbishop Carlo Maria Vigano claimed the pontiff had himself ignored abuse allegations against prominent US cardinal Theodore McCarrick for five years.
Francis, currently on a tour of the Baltics, has so far refused to respond to the allegations.
He has however announced a Vatican meeting of heads of episcopal conferences on the protection of minors, for February 2019.
Jörg Schuh of the Berlin-based Tauwetter centre for victims of sexual abuse told AFP TV that "the Catholic Church has a global problem".
"I would like the Pope to make it his number one topic, and for his Church to really work on it," he said.
Major abuse cases in Germany have included a Berlin elite Jesuit school which admitted to systematic sexual abuse of pupils by two priests in the 1970s and 1980s.
Last year, the world-famous Catholic choir school the Regensburger Domspatzen revealed that more than 500 boys there had suffered sexual or physical abuse which one victim likened to "prison, hell or a concentration camp".
The brother of former Pope Benedict XVI, Georg Ratzinger, who led the choir school from 1964 to 1994, said he was not aware of sexual abuse and rejected claims he did too little to shed light on the tragedy.
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