Netanyahu also vowed to advance a bill aimed at preventing foreign governments from funding non-profits.
Netanyahu said that Israel views Michel’s meeting with “Breaking the Silence and B’Tselem” on Wednesday with the "utmost gravity."
“The Belgian government needs to decide whether it wants to change direction or continue with an anti-Israel line,” he said.
B’Tselem documents alleged human rights violations against the Palestinians, and Breaking the Silence publishes critical soldiers’ testimonies of Israeli military practices against the Palestinians.
B’Tselem is the Israeli Information Center for Human Rights.
Netanyahu also vowed to advance a bill aimed at preventing foreign governments from funding non-profits that he said harmed Israeli military soldiers.
Michel, who arrived in Israel on Sunday for a three-day trip, met with Netanyahu on Tuesday, a day after Israel passed a controversial law retroactively legalising Israeli settlement in the West Bank.
Belgium was one of several countries that condemned the law, and called on Israeli leaders not to implement it, and describing it as an obstacle to peace and dangerous to a possible two-state solution.
Israel passed a so-called transparency law last year that demands that all groups getting more than half their funding from foreign governments must publish the names of those specific governments.
Israeli critics campaigned for months against the bill, charging that it targets liberal advocacy groups and seeks to “silence” any rights organisations that do not follow the conservative government line.