Filoni criticized those who "run the risk of rowing out of sync within the ship of Peter" and of leading the Chinese faithful into misunderstanding the agreement.
"Only with a superficial spirit or in bad faith could one imagine that Pope Francis and the Holy See would abandon the flock of Christ, wherever or in whatever condition it finds itself in the world," Filoni said.
"Therefore, we must continue to work to improve the perception of the faithful, who are often influenced by media messages that are not altogether correct or balanced and find it difficult to understand the due discretion that surrounded the dialogue between the Holy See and the People's Republic of China," he continued.
"The Pope, together with his coworkers, has done, is doing, and will do all that is possible to be close to the Church in China. Our methods are not infallible, but we truly love the Church and the Chinese people," Filoni said.
Filoni said that he hopes "not to hear or read about local situations in which the Agreement is exploited to compel people to do what is not even required by Chinese law, such as joining the Patriotic Association."
"In the sixty years since the creation of the Patriotic Association, everyone, in perhaps an unequal and dramatic way, has suffered, both in a physical and moral sense," he said.
"It is the Lord who guides history. Therefore, I would hope that, first of all, in dealing with any possible dilemmas, they would know always how to see the other with trust, even if some aspects of the current situation are perceived as injustices and with difficulty," Filoni said.
Zen responded, "His Eminence loves to have legitimate reservations about what the Holy See does, but in the meantime he accuses me of not rowing in harmony with the barque of Peter."
Several Chinese bishops participating in the Chinese People's Political Consultative Conference (CPPCC) also spoke out about the Vatican-China agreement this month.
The theme of this year's CPPCC assembly meeting is "the study and application of Xi Jinping's thinking on socialism with Chinese characteristics for a new era."
Bishop Vincent Zhan Silu of Mindong (Ningde), a member of the CPPCC, told Chinese press at the meeting, "There will be no official or unofficial Church when the Church is united," reported UCA News.
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Mindong is one of two dioceses in China in which an underground bishop was asked to step down to be replaced by a formerly excommunicated bishop.
Pope Francis reportedly asked the former bishop of Mindong to step down in obedience and "in sacrifice" so that Chinese government-appointed Bishop Zhan could take his place through a letter signed by Cardinal Filoni and Vatican Secretary of State Pietro Parolin.
In response to a question about what this would mean for the underground church, Zhan responded, "Don't you want the Church to be united? A Church schism is not the fundamental aspiration of Catholics."
Cardinal Zen questioned, "Can the gentlemen at the Vatican tell us what we have gained with that agreement? Is it true that the Chinese communists have finally recognized the authority of the pope? Has the spokesperson of the Patriotic Association and the bishops' conference not publicly declared that they will maintain the principle of the independent Church and that they will follow the leadership of the Party?"