The paper describes Catholic Pope Benedict XVI as incompetent and unwilling to promote interfaith dialog between Protestants and Catholics. It also finds fault with the Catholic leadership in Germany for failing to take a consistent approach to the interpretation of church dogma.
On Wednesday, a crisis meeting of the leaders of the two denominations resulted in apologies but also in the growing realization that the cracks between the two have only been papered over.
The meeting lasted more than two hours, and, according to the head of the German Protestant Church, Wolfgang Huber, succeeded in re-establishing a level of trust.
"The Protestant Church considers this paper a mistake," Huber said. "We extend our apologies to all Catholics who rightly feel personally insulted by what was written there."
Huber said the paper had not been authorized and had been compiled by a senior policy consultant in the Protestant Church leadership and leaked to the media.
The paper speaks of major tensions between the denominations since Pope Benedict came to power in 2005. It says this friction could be the result of either the Vatican's inability to conduct interfaith dialog or as an indication of a change in papal policy.
"Worsening atmosphere"
The paper also compares the leader of the German Catholic Church, Archbishop Robert Zollitsch, to a boxer reeling in the ring from the blows of his opponent.
Zollitsch, it says, staggers between openness and the hard-line policy insisted upon by the Vatican.
Zollitsch himself dismissed the accusations but admitted that problems exist.
"This paper is full of cliches that don't reflect the real situation," Zollitsch said after the meeting with Huber.
"Of course there are theological differences with the Protestant Church, but our meeting wasn't about these problems. It was about a worsening of the atmosphere between us which we hopefully will be able to improve."
Rudolf Lill, an expert in Vatican policy, said the rift is the result of policy pursued by Pope Benedict, who has shaped as a hard-line enforcer of Church dogma rather than a religious reformer.
"In some aspects the author of the paper is quite right," Lill said.
"Papal policy under Benedict has been marked by a drive for absolute power, which in turn will limit the influence of the Roman Catholic Church in contemporary society. This year would appear to be a landmark year in this respect."
As evidence of this, Lill points to the pope's recent decision to lift the excommunication of Bishop Richard Williamson, the head of the ultra-traditionalist St Pius Brotherhood and a known Holocaust denier.
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SIC: DW