According to The Jerusalem Post newspaper, the Israeli Foreign Ministry condemned the move and summoned the EU ambassador.
"This latest action raises questions about the role the European Union wishes to play, and it is liable to have consequences on relations between the EU and Israel," the ministry said.
Several high-ranking Israeli politicians also criticized the decision, according to the news outlet.
The Golan Heights, internationally recognized as Syrian territory, was seized by Israel during the Six-Day War in 1967. In 1981, the Israeli parliament voted to annex two-thirds of the region.
Palestinian territories of East Jerusalem, West Bank and the Gaza Strip were also claimed during the war. Palestinians seek the recognition of their independent state, proclaimed in 1988, on these lands.
Israel has continued to build settlements in the occupied territories, prompting condemnation from the United Nations.