Merz, after stopping in Jordan for talks with King Abdullah II, is set to fly on to Israel in the evening before meeting Prime Minister Benjamin Netanyahu in Jerusalem on Sunday.
The German leader is also expected to visit the Yad Vashem Holocaust memorial.
Given the dark legacy of Nazi Germany's industrial-scale murder of Jews, German leaders have long seen unflinching support for Israel as a bedrock of the country's foreign policy.
In a speech in September celebrating the reopening of Munich's synagogue, which was severely damaged by the Nazis, Merz visibly struggled to hold back tears, his voice breaking.
But Israeli-German ties were shaken during the Gaza war set off by the October 7, 2023 Hamas attack on Israel, the deadliest in the country's history.
Merz, who took power in May this year, has repeatedly criticised Israel's relentless military campaign, which has killed tens of thousands of Palestinians.
In August, he also moved to restrict sales of weapons for use in Gaza.
Since a fragile US-backed ceasefire and hostage deal ended full-scale fighting, Germany has lifted those export restrictions.
Despite the ceasefire deal, more than 350 Palestinians have been killed in Gaza, according to local health authorities, as well as three Israeli soldiers.
The UN also warns that Israel is still not allowing enough aid into Gaza.
Before leaving Berlin on Saturday morning, Merz spoke with Palestinian Authority (PA) President Mahmud Abbas.
A spokesman said Merz underscored German support for a two-state solution but urged Abbas to push through "urgently necessary reforms" of the PA in order to play a "constructive role" in the postwar order.
'Signal of support'
After the recent strains, Israel expects a "signal of continued support" from Merz, said Michael Rimmel, head of the Jerusalem office of the Konrad Adenauer Foundation, affiliated with Merz's centre-right Christian Democrats (CDU).
German-Israeli relations have been strained over the past two years but remain "better than many people think", Rimmel told AFP.
But he said Berlin has little discernible influence on Netanyahu's government, which has pushed on with West Bank settlements despite protests from Berlin and elsewhere, and dismissed calls for a two-state solution.
"Certainly, President Trump and the Americans have greater influence," said Rimmel, noting that the US president was able to pressure Netanyahu into the Gaza ceasefire.
Gil Shohat, head of the Tel Aviv office of the Rosa Luxemburg Foundation, which is affiliated with Germany's far-left Die Linke party, sharply criticised Merz for making the trip.
Shohat argued that Merz is effectively offering political support to Netanyahu and Israel's hard-right government.
"Netanyahu is a wanted war criminal and is under suspicion of corruption," said Shohat. "Going there now and legitimising him is a fatal sign of normalisation in a situation that must not be normalised."
Defence deals
Although Merz's public criticism of Israel was unusual for a German leader, it was measured by international standards.
Merz recently offered Israel full-throated support as European broadcasters weighed whether to exclude the country from the annual Eurovision Song Contest, calling such a possibility "scandalous".
The decision to include Israel in the upcoming Eurovision event, reached on Thursday, was warmly welcomed in Berlin even as it prompted boycotts from Spain, the Netherlands and elsewhere.
Still, despite the close ties, German officials have said there are currently no plans to invite Netanyahu -- who faces an international arrest warrant for war crimes in Gaza from the International Criminal Court (ICC) -- to Berlin.
Merz, not long after his party's election victory in February, vowed to invite the Israeli leader and told him in a phone call that he would not be arrested.
Any tensions in German-Israeli relations have also not disrupted key military ties. Germany last week put into operation the first phase of the Israeli-made Arrow missile defence shield.
The $4.5 billion deal was reportedly the largest arms export agreement in Israeli history, and Berlin has also turned to Israeli firms for help in drone defence.
The German-Israeli Society -- which said Merz's visit must aim to "repair the damaged German-Israeli relations" -- also pointed out that defence ties "have long since reversed".
"Israel is no longer dependent on German technology, but rather German defence depends on Israeli technology."
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