Netanyahu had scrapped talks with Sigmar Gabriel at the last minute, after Germany's top diplomat pressed on with plans to meet with Israeli rights groups Breaking The Silence and B'Tselem.
In an interview with Germany's biggest selling Bild daily, Netanyahu defended his decision.
"Foreign diplomats are welcome to meet with civil society activists and members of the opposition and anyone else they'd like," he said.
"But my red line is that I will not meet diplomats who come to Israel and lend legitimacy to fringe radical groups that falsely accuse our soldiers of war crimes and undermine Israeli security," he added.
"These are the days we mourn the murdered members of our people in the Holocaust and our fallen soldiers. The Israeli army is the one force that keeps our people safe today," he said.
Netanyahu's decision to cancel the meeting with Gabriel was a rare step, but in line with the current right- wing government's stance against groups it accuses of having political agendas and unfairly tarnishing Israel.
However, tensions have grown as Netanyahu has irked Berlin by pressing on with settlement building in the Palestinian territories despite repeated warnings from world powers that it would harm any prospects for peace.
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