His comments came after the European Union decided to forbid funding of projects in territories Israel has occupied since 1967 --East Jerusalem, the West Bank and the Golan Heights.
"If the Europeans carry on this way they will have achieved the opposite result and pushed us away from peace talks," he said.
Elkin said the EU's pressure should be directed at the Palestinians, not Israel.
"We are ready to negotiate. We're not the problem," he said.
Science Minister Yaakov Peri estimated 40 percent of Israeli institutions' budgets will be affected by the EU's decision, Ynetnews.com said.
Ministry officials also said universities whose studies involve matters beyond Israel's demarcation lines could also suffer.
"In fact, the decision sets a clear political border to any academic institute in Israel and prevents them from collaborating with researchers, institutes, and even statistical data from beyond the Green Line," ministry officials said.