Israel has circumvented the potential damage of an academic boycott with the signing of a new European Union agreement that allows the nation’s scientists to take part in the next six-year research programme.

The agreement, worth nearly £34bn, comes amid continued and heated debate over the vote in May by the University and College Union to consider a call from Palestinian trade unions to boycott Israeli universities.

Academic boycotts have been widely condemned by university and science leaders, including Universities UK, the vice-chancellors’ group, and the Royal Society, the UK’s academy of science, which warned that boycotts infringed academic independence and the free exchange of ideas.

By securing access to the &#euro;50bn (£33.8bn) Seventh Research Framework Programme (FP7), which runs from 2007 to 2013, Israel has avoided the most serious potential threat to its universities.

The European Union is Israel’s second biggest source of research funding, after the Israeli Science Foundation. Israel will be is a key player in FP7, being the only nation outside of the EU participating in a major public-private research partnership to develop green air transport to be funded under the programme.

Israel’s participation in European research programmes was called into question in 2002 when two British academics had a letter published in the Guardian advocating a moratorium on all grants and contracts to Israel from European cultural and research institutions.

Janze Potocnik, the EU’s research commissioner, said: “Israel’s association to the framework programme has proved to be of mutual benefit for both sides over the last couple of years. Whereas the European research area will benefit from the renowned excellence of the Israeli research community, Israel will gain full access to the biggest research programme in the world.”

Under today’s agreement, Israel will contribute around &#euro;440m (£297.6m) to the FP7 budget and Israel universities and companies will be allowed to compete for FP7 research projects on a footing to their counterparts in Europe’s member states. The agreement renews a deal between Israel and the EU that allowed the nation to participate in previous EU research framework programmes. The programmes fund collaborative projects.