Speaking at the annual toast to the New Year in Jerusalem, Netanyahu said the EU was more critical in its judgment of Israel compared to other countries.
"There is a natural tendency in the EU establishment to single out Israel and treat it in ways that other countries are not being dealt with, and especially other democracies," he said.
Acknowledging the breakdown in relations between the EU and Israel, Netanyahu called for a "reset" in bilateral relations.
There has been an ongoing deterioration in the relationship between the EU and Israel, which many believe was largely sparked by 2014 offensive of Gaza, which resulted in more than 2,200 Palestinian casualties.
Video: Prime Minister Benjamin Netanyahu's Speech at GPO's Annual Meeting with the Foreign Press https://t.co/kEQrM8IkoF— PM of Israel (@IsraeliPM) January 15, 2016
Israel was further incensed at an EU decision to specifically label exported items coming from Israeli settlements in the Palestinian Occupied Territories.
Israeli-Swedish Ties Highly Strained
On top of criticism of the EU as a whole, Netanyahu also has also taken aim at Sweden, in particular Foreign Minister Margot Wallstrom, labeling her calls for an independent probe into the killing of Palestinians as "absurd" and "stupid."
During an address to Swedish parliament in December, Wallstrom raised concerns over the prospect of heavy-handed reprisals against Palestinian people due to the recent spate of knife attacks.
"The response [to Palestinian attacks] must not be of the kind — and this is what I say in other situations where the response is such that it results in extrajudicial executions or is disproportionate in that the number of people killed on that side exceeds the original number of deaths many times over," Wallstrom said.
However, Netanyahu, who interpreted Wallstrom's speech as an accusation that Israel was carrying out "extrajudicial executions" was highly critical of Stockholm.
"It's outrageous, it's immoral and it's stupid […] People are defending themselves against assailants wielding knives who are about to stab them to death and they shoot the people — and that's extrajudicial killings?" he said.
Since the beginning of October there have been near daily attacks on Israeli citizens from people armed with knives or other weapons. About 150 Palestinians have been killed as a result, with Israeli officials saying that more than 90 of those were assailants, while others were killed in clashes with security forces.
Since October, the Palestinian attacks have led to the deaths of 24 Israeli citizens and one American.