When the university and college lecturers' union, the UCU, voted at its conference in May this year to have a debate on an academic boycott of Israel, all hell broke loose. British academia was criticised by many commentators in the UK, and by professors around the world, for anti-Semitism and for inhibiting the free flow of ideas.

In August a full-page advertisement appeared in The New York Times signed by 286 American university presidents, including the bosses of MIT and Princeton. Headlined "Boycott Israeli Universities? Boycott Ours, Too", it contained an eloquent statement by Lee Bollinger, a noted free speech lawyer and president of Columbia University in New York. He said: "In seeking to quarantine Israeli universities and scholars, this vote threatens every university committed to fostering scholarly and cultural exchanges that lead to enlightenment, empathy and a much-needed international marketplace of ideas."

The row was deeply embarrassing to the British Government. So Bill Rammell, the higher education minister, and Drummond Bone, the former president of Universities UK, paid a visit to Israel and the Palestinian Territories to lower the temperature and to reassure Middle Eastern universities that the United Kingdom was committed to promoting dialogue rather than boycotts.

Rammell and Bone promised that a small group of university vice chancellors would visit again to look in detail at how to strengthen links between British universities and those in Israel and the Palestinian Territories. That trip took place last week when four university chiefs from England, Wales and Scotland flew out for further talks with their opposite numbers in the Middle East.

Their job had been made easier by the fact that the UCU had received legal advice saying that an academic boycott of Israel would be unlawful and could not be implemented. "I think we were able to reassure the Israelis," said Professor Rick Trainor, president of Universities UK and leader of the group. "They responded positively to what we said about the boycott. The situation of the universities in the two countries is very different but the common theme of both sides was that they were very pleased at the prospect of increased academic contact."

Trainor, who was accompanied on the three-day trip by Professor Antony Chapman, vice chancellor of the University of Wales Institute, Cardiff, Professor Anton Muscatelli, principal of Heriot-Watt University, and Professor Paul O'Prey, vice chancellor of Roehampton University, made it clear to the Israelis that the delegation was not taking a stand on the dispute. "We said that we were taking a stand on academic freedom against the boycott," he explained.

"We were always against it and it's fortunate that the UCU have taken the view that they won't be proceeding with the debate on the boycott."

British universities can do little on their own to solve the Israeli-Palestine conflict, but by improving links with institutions in the Middle East they are hoping to foster cooperation and understanding. With eight universities and many other academic institutions and teacher training colleges, Israel has a highly developed higher education system. Albert Einstein was one of the founders of the Hebrew University in Jerusalem and the Technion (Israel Institute of Technology) has two Nobel prize winners. More than half of 20- to 24-year-olds are enrolled in higher education.

It is in the interests of UK universities to increase contact with such a successful player, according to Trainor, who is principal of King's College London. "It is not for us to decide what will happen," he said.

"What we will be recommending is that more research be put into academic links both with Israel and the Palestinian Territories."

The universities in the Palestinian Terrorities provide a stark contrast to those in Israel. The British university chiefs were able to see how tough things had been, and still were, for them. They visited An-Najah University in Nablus and Birzeit University, near Ramallah, which was closed for 51 months, from 8 January 1988 until 29 April 1992, and had to operate underground with small study groups. They also talked to senior staff of Al-Quds University in Jerusalem, which has only been able to continue operating this academic year through donations from overseas. And they were told how difficult it was for academic staff or students to get around, to leave the West Bank, for example, to go abroad.

They were also told about the difficulties involved in the daily business of getting to university. The army checkpoints mean that students, academics and other university employees sometimes have to make very long journeys – of as much as two hours in each direction every day.

All the Palestinian universities have severe financial problems and some months are unable to pay their staff. "But we were struck by the very considerable potential of the Palestinian institutions," said Trainor. "They're doing a great job of carrying on despite the security situation."

The one thing these universities wanted was to be less isolated from the international academic community, according to Trainor. The British delegation talked to the Palestinians about the possibility of short-term visits by UK academics and increasing the number of scholarships for Palestinian students to come to Britain.

Many of the senior Palestinian staff the VCs met had been trained and educated in Britain and the US and pointed out that the generation coming up behind them had not had these opportunities. They hoped that ways could be found to get junior academics as well as students to the UK so that they could study for PhDs and undertake postdoctoral work in the West.

The report that the vice chancellors are writing will go to the Department for Innovation Universities and Skills with a strong recommendation that contact with Palestinian and Israeli universities be actively and further encouraged. Links do exist but the VCs' visit has uncovered a need for the British government and universities to do more in the interests of both this country and the Middle East.