The European Union, along with much of the international community, considers Israeli settlements in the West Bank and east Jerusalem illegal and an obstacle to the establishment of a Palestinian state.
The Palestinians want those territories, along with the Gaza Strip, for their future state. Elkin said the EU compromise also included an Israeli statement objecting to the European position on settlements.
Elkin added that Israel would compensate institutions that are ineligible for the EU funding because they are located in the occupied territories.
The "Horizon 2020" program enables participants to apply for funds for research and collaboration in areas such as climate change, renewable energy and food safety. The EU has budgeted more than 70 billion euros ($95 billion) for the program, which is to run from 2014 to 2020. Officials estimate that Israel could gain more than 300 million euros ($400 million) from the complicated funding system over the seven-year period.
The EU's top diplomat in Israel, Lars Faaborg Andersen, called the compromise excellent news. "It will allow the EU and Israel to continue their mutually beneficial partnership in science and technology," he said in a statement.
Palestinian official Nabil Shaath praised the Europeans for sticking to their opposition to the settlements. "It's time for the Israelis to understand that all the international community is against settlements," he said.
The Israeli daily newspaper Haaretz said that despite the last-minute compromise, the spat with the EU indicated that Israel "is now beginning to pay the price of its deeds in the occupied territories."
"The settlement enterprise has turned Israel into an immoral state whose policies are unacceptable to the world of which it seeks to be part," it said in an editorial.