BERLIN — Growing up as a teenager in Germany, Jonathan Logan’s opinion of the Middle East conflict was black and white. “The Israelis were the good ones, and the Palestinians very clearly the bad ones,” he recalled Wednesday, as Prime Minister Benjamin Netanyahu of Israel arrived here for previously scheduled and suddenly rather tense consultations with Chancellor Angela Merkel.

That pro-Israeli attitude was, Mr. Logan said, “what you always get from the mainstream.” Now 23 and a promoter for German television, he said his views had shifted. “A Palestinian shoots a rocket, and Israel answers with a fighter jet,” he said. “Both sides kill civilians. It doesn’t matter which side kids are on.”

The complex relationship between Israel and Germany carries tremendous baggage, built as it is on a historic crime, on notions of guilt and redemption. Now that relationship is being tested by the growing discord over the peace process that has already divided Israel from much of the rest of Europe. That test comes as the underpinnings of the relationship grow looser and as the generation of perpetrators and survivors of the Holocaust begins to disappear, 67 years after the end of World War II.

Last week at the United Nations General Assembly, Germany chose to join 40 other nations in abstaining from a vote on upgrading the status of Palestinians to nonmember observer state. Germany’s decision had no effect on the outcome, with 138 nations voting for the proposal and 9 against. For any other nation, with the exception of the United States, the vote would have been little more than a footnote.

But when it comes to Israel, Germany will never be just any other nation. There might never have been an Israel if not for the waves of refugees fleeing the Nazis followed by Holocaust survivors.

Mr. Netanyahu considered Germany’s abstention significant enough that he criticized Ms. Merkel, his hostess for dinner on Wednesday evening, in a German newspaper a few hours before his plane landed at Tegel airport here.

He told the German newspaper Die Welt that it would be “disingenuous if I hid the fact that I, like many in Israel, was disappointed by the German abstention at the United Nations.”

Increasingly isolated and under heavy criticism in Europe, the Israeli government expected Germany to have its back.

Mr. Netanyahu’s comments were not just the latest evidence of a growing rift between the longtime allies, but also expressed an unspoken fear that a more substantial shift might be under way in Germany.

“Historic responsibility is no longer sufficient,” said Reinhold Robbe, a former member of Parliament from the Social Democratic Party and head of the German-Israeli Society. “With so many young people and people with a migration background with no connection to the Holocaust and no sense of responsibility.”

To understand the fear of isolation behind the Israeli disappointment, it helps to look at the short list of countries that supported Israel and the even shorter list of influential ones: the United States, Canada, the Czech Republic, the Marshall Islands, Micronesia, Nauru, Panama and Palau.

A country like Germany, the biggest in the European Union, would have been a welcome addition for Israel.

Frustration with Israel has only grown in Europe since the announcement that the government had approved 3,000 more units of housing in contested areas of East Jerusalem and the West Bank and was resuming planning and zoning work in the contentious area known as E1. The announcement was viewed as a reaction to the United Nations vote, and critics said that future construction in E1 could irreparably harm the chances for a viable, contiguous Palestinian state there.

Germany stopped short of summoning the Israeli ambassador to complain about the plan, as several other European governments did, including Britain and France. But Ms. Merkel’s spokesman, Steffen Seibert, said Monday that the move on the settlements sent “a negative message,” and that Israel was “undermining trust in its readiness to negotiate.”

There is strong support in Germany for a two-state solution to the dispute between Israelis and Palestinians. The plans for E1 have brought even more condemnation elsewhere in Europe. Germans are increasingly joining in.

In the German newspaper Der Tagesspiegel, a former Israeli ambassador to Germany, Shimon Stein, described “the gulf between German politics and German public opinion as reason for concern.” Mr. Stein said that Ms. Merkel should be clear in her criticism of Israeli policy and bring Mr. Netanyahu’s attention to “the negative sentiment against Israel in Germany and in other parts of the E.U.”

Not everyone believes a significant shift is in motion in Germany. “Public opinion about Israel has slipped somewhat, but I think it’s going too far to say there’s been an erosion of support,” said Deidre Berger, director of the Berlin office of the American Jewish Committee, an advocacy group that supports Israel. “It goes up and down in terms of attitudes toward Israel.”

Ms. Merkel received a prize last week from Berlin’s Jewish population. She had taken a strong stance this year in supporting legislation to safeguard the right of parents to circumcise their male children, after a regional court in Cologne ruled ritual circumcision constituted bodily harm to minors. But the award was also for contributing to the security of the state of Israel and the improvement of ties between Israel and Germany.

“We are not neutral,” Ms. Merkel told the audience. The next day, Germany abstained in the United Nations vote.

Nina Müller, on her way to pick up her daughter at a Berlin day care center on Wednesday, said it still was not possible for Germany to be more critical toward Israel. “Because of its history, Germany is always cautious and diplomatic,” she said. “You can’t allow yourself to be very critical, even about things that in another situation you might see differently.”