ROME – Although agreeing with him that the clerical abuse crisis a “catastrophe,” Pope Francis rejected the resignation presented to him by German Cardinal Reinhard Marx as archbishop of the archdiocese of Munich.

“You tell me that you are going through a moment of crisis, and not only you but also the Church in Germany is going through it,” Francis wrote in a letter dated June 10. “The whole Church is in crisis because of the abuse matter; moreover, the Church today cannot take a step forward without addressing this crisis.”

The “ostrich policy” of hiding the head in the sand leads nowhere, the pope argues, and the only way to address the crisis is to address it “from our paschal faith.”

The Catholic Church in Germany has long been struggling to address the clerical abuse crisis, with several top-ranking officials, including Marx and Cardinal Rainer Woelki of Cologne, accused of mishandling allegations.

Marx, 67, had offered his resignation to Pope Francis on May 21 despite being eight years shy of the mandatory retirement age of 75. In his letter, the prelate said that he wanted to take his share of responsibility for the “catastrophe of sexual abuse” by representatives of the Catholic Church.

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Marx is a member of the cardinals who advice the pope on the reform of the Roman curia and has long been perceived as an ally to the Argentine pope.

Under church law, a bishop may offer his resignation, but it’s always up to the pope to the decide whether or not to accept it. Through Thursday’s letter, the pope made it clear that he’s not accepting it.

“If you are tempted to think that, by confirming your mission and not accepting your resignation, this Bishop of Rome (your brother who loves you) does not understand you, think of what Peter felt before the Lord when, in his own way, he presented him with his resignation: ‘Depart from me, for I am a sinner’, and listen to the answer: ‘Shepherd my sheep’.”

“First of all, thank you for your courage,” Francis writes in a letter that was written in Argentine informal Spanish, which has grammatical differences from that spoken in other countries, making it clear that he penned the letter himself. “It is a Christian courage that does not fear the cross, does not fear to be humbled before the tremendous reality of sin.”

The pope tells Marx he was right in describing the abuse crisis as a “catastrophe” and acknowledged the “sad history of sexual abuse and the way the Church dealt with it until recently. To realize this hypocrisy in the way of living the faith is a grace, it is a first step that we must take.”

“We have to take charge of history, both personally and as a community,” Francis wrote. “We cannot remain indifferent in the face of this crime. To assume it supposes to put ourselves in crisis.”

Owning up to the history of abuse, both individually and a s community, Francis told Marx, means that even though its correct to interpret historical situations with the hermeneutics of the time in which they happened, this does not “exempt us from taking charge and assuming them as history of the ‘sin that besieges us’.”

“Therefore, in my opinion, every bishop of the Church must assume it and ask himself what should I do in the face of this catastrophe?” Francis wrote.

There’s a growing number of voices, particularly among experts in the Church’s fight against clerical sexual abuse, who claim that the majority of the bishops who have been in office for more than ten years have at one point or another mishandled a case of abuse.

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The Church, the pope insists, will not be saved by its own prestige, “which tends to conceal its sins,” nor by the power of money and the opinion of the media – noting that often “we are too dependent on them.”

“It is urgent to ‘ventilate’ this reality of abuses and of how the Church proceeded, and let the Spirit lead us to the desert of desolation, to the cross and to the resurrection,” Francis wrote. “It is the path of the Spirit that we must follow, and the starting point is humble confession: We have made a mistake, we have sinned. Neither the polls nor the power of institutions will save us.”

Follow Inés San Martín on Twitter: @inesanma