Gabriel said it would be a "remarkable event, to put it mildly," if Netanyahu cancelled their planned talks, arguing it was normal to talk to civil society representatives.
"Imagine if the Israeli Prime Minister came to Germany and wanted to meet people critical of the government and we said that is not possible.That would be unthinkable," he told Germany's ZDF television.
A German foreign ministry spokeswoman had said the minister was due to meet civil society groups but declined to identify them.
Germany sees itself as one of Israel's closest allies, but the legacy of the Holocaust means their ties are highly charged, and in recent years Berlin has been increasingly critical of Israel's settlement plans.
Israeli media said Gabriel would meet with "Breaking the Silence," a group that collects testimonies from Israeli veterans about the military's treatment of Palestinians in the occupied West Bank and the influence it says Israeli settlers have on the army's actions.
Israeli Environment Minister Zeev Elkin, a confidante of Netanyahu, told Israel radio it was "unthinkable" for a minister to meet groups working against the country he was visiting.
"The time has come for us to put an end to this situation in which anyone can come and meet groups that act against Israel ... you are entitled to meet whoever you want, but don't expect that all the leaders of the state will stand in line to meet you," he said.
Both organisations have become popular targets for right-wing politicians, who accuse them of damaging Israel's reputation abroad and putting Israeli soldiers and officials at risk of prosecution.
Gabriel, a Social Democrat who has spoken publicly about a rift with his father, a convinced Nazi, is visiting the Middle East to press for a two-state solution to end the conflict between Israelis and Palestinians.
Germany in March cancelled an annual meeting of German and Israeli leaders that was to take place in May amid rising frustration in Berlin with settlement activity in the Israeli-occupied West Bank.
In 2016, Israel passed a law requiring non-government organizations that receive more than half their funding from foreign governments or bodies to provide details of their donations.
The legislation was largely seen as targeting left-wing organisations such as Breaking the Silence and B'tselem, and it drew international criticism.
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