In a letter to the head of Jerusalem's Yad Vashem Holocaust memorial, Cardinal Karl Lehmann said it was inappropriate to "connect contemporary problems or situations of injustice in any way with the National Socialists' genocide of the Jews."
The letter from Germany's senior cardinal, who is head of the German conference of bishops, to Yad Vashem director Avner Shalev was made public late on Wednesday.
According to the daily Sueddeutsche Zeitung, the bishops made the remarks after meeting Christian Palestinians in Bethlehem, in the occupied West Bank, and visiting a children's
Having listened to a nurse explain the difficulties mothers faced because of local security restrictions, Bishop Gregor Maria Hanke vented his anger to journalists, the paper said.
"In the morning we see the photos in Yad Vashem of the inhuman Warsaw ghetto, in the evening we drive to the ghetto in Ramallah. It really makes you mad," the paper quoted him saying.
Hanke, one of a party of 27 German bishops on the pilgrimage in early March, said many bishops were deeply affected by the "existential drama" they witnessed.
The paper reported Hanke as saying "yes, to Israel's right to exist -- but it cannot be that this right to exist is so brutally asserted that another people is unable to live."
His colleague Bishop Walter Mixa described the conditions as a "Ghetto-like situation... bordering on racism," the paper said.
Israel says security concerns are behind the network of military checkpoints it has established in the West Bank. Palestinians and human rights groups call Israeli travel restrictions collective punishment.
Cardinal Lehmann's criticism of the bishops was made public a day after a letter from Shalev, in which he said the remarks illustrated "a woeful ignorance of history and a distorted sense
"These unwarranted and offensive comparisons serve to diminish the memory of victims of the Holocaust and mollify the consciences of those who seek to lessen European responsibility for Nazi crimes," he wrote in the letter.
Israeli media also strongly condemned the remarks.
In an opinion piece for Israel's biggest paper Yedioth Ahronoth, correspondent Eldad Beck said the comments raised the question of "just how tainted with anti-Semitism... the Catholic
church and German society remained."
Lehmann said the bishops had since clarified they did not intend to make comparisons between 'then' and 'now'.
"The German bishops remain aware of their historical responsibility," he added in the letter. "We know we have to show this by being sensitive in our choice of words."