He said: "Unfortunately, this instruction is such a strong brake on the motivation and appreciation of the ministries of lay people that I am very concerned about how we are to find new committed Christians under such conditions and how we can continue to accompany and support our pastoral workers well."
He also defended the German Church's controversial "Synodal Way," which is bringing together lay people and bishops to discuss four main topics: the way power is exercised in the Church; sexual morality; the priesthood; and the role of women.
He said: "This makes our 'Synodal Way' in Germany all the more necessary, since it is precisely these ecclesiological questions that are at stake, the question of what a 'Church of participation' can look like, how priestly ministry is to be understood and to exist today, and how women and men shape the Church together. Only this synodal way can be an answer to this Roman challenge."
Bishop Peter Kohlgraf of Mainz claimed that the instruction represented an "interference" in his episcopal ministry that he "could not quite accept so easily."
In a statement on Wednesday, he said that instruction called into question plans to merge parishes in his diocese as part of a project known as the "Pastoral Way."
From the beginning, he explained, the "Pastoral Way" was conceived as a "spiritual way."
"The central spiritual question is how the message of the Gospel can be lived and proclaimed under today's conditions. This is not possible without looking well at the 'signs of the times' and interpreting them in the spirit of the Gospel," he said.
He lamented that every merger would apparently require approval by the Vatican, which he said was likely to reject plans to appoint lay people to administer merged parishes.
"The administrative directors we are planning are probably not appropriate according to Roman ideas," he said, expressing concern that priests in his diocese would be overburdened with bureaucracy.
A spokesperson for the German bishops' conference said the Vatican instruction would be "studied carefully" and discussed at a forthcoming meeting.