"I do not feel I know for sure what happened, either at Tantura or at Haifa..."

"I have read many hundreds of related articles, interviews and documents ...talked in detail to many of those most closely involved. And I do not feel I know for sure what happened, either at Tantura or at Haifa... so how can the members of the AUT, after just a few minutes' hasty debate, seem so confident that they do?"

The AUT's decision to boycott two Israeli universities over alleged 'illegal activities' was rash and possibly misguided, believes Stephen Howe

The night before the Association of University Teachers voted to boycott Haifa and Bar-Ilan universities, I had dinner with two close friends. Both teach at Haifa, both, as it happens, are Arab - one Palestinian Muslim and one Druze - and both were centrally involved in the events that are the stated justification for the boycott. Yet no one from either side of the AUT's debate had sought their opinion. In fact, until I showed it to them, neither had even seen the text of the two resolutions. The boycott's proposers - and their critics - have relied on a narrow and partisan range of informants, especially about happenings at Haifa.

Bar-Ilan University, near Tel Aviv, became a target of the British boycott because of its association with the Judea and Samaria College in Ariel, one of the biggest Jewish settlements on the occupied West Bank. It is Israel's only specifically religious university, committed to "Jewish heritage" and Torah education, but it offers a broad range of academic subjects and its teachers include strong critics of the state, most notably the political scientist Menachem Klein.

Since the mid-Nineties, small numbers of Judea and Samaria students took degree courses validated by Bar-Ilan, thus involving the university - as pro-boycott campaigners argue - in direct collaboration with Israel's occupation of the land where the college operates. The university authorities have responded to their critics by stating that their agreement with the college is set to end this year.

The case of Haifa University is more complex. It is a dispute over academic freedom and integrity that goes to the heart of the Israeli-Palestinian struggle and the nature of Israel's very identity. Haifa has long had a left-wing reputation, while its proportion of Arab students and faculty is the highest in the country. At first glance, it is an unlikely place to be singled out.

But the AUT resolution tells a different story. It notes: "On May 15, 2002, Dr Ilan Pappe, senior lecturer in political science at Haifa University, was sent a letter notifying him that he faced trial and possible dismissal from his position. The charge was that he had violated 'the duties of an academic member of staff', and had 'slandered departments and members in the humanities faculty, damaged their professional reputation and endangered the possible promotion of some of them'.

"These accusations related to Dr Pappe's efforts to defend a 55-year-old graduate student, Teddy Katz, whose masters thesis was under attack by an Israeli veterans' organisation because it documented a massacre of 200 unarmed civilians by the Haganah (the pre-state army of Israel) at a village called Tantura, near Haifa. The recriminations are still continuing and Dr Pappe's job is still being threatened."

The AUT resolved "to call on all AUT members to boycott Haifa University until it commits itself to upholding academic freedom and, in particular, ceases its victimisation of academic staff and students who seek to research and discuss the history of the founding of Israel".

The story begins in 1999 when Katz, a veteran kibbutznik and peace activist, was awarded his Haifa MA. His thesis was a study of events during the 1948 war that concentrated on the fate of two Palestinian villages, Umm Zaynat and Tantura. Relying heavily on oral testimony - interviewing 135 Israeli and Palestinian participants - Katz believed he had uncovered a hidden massacre. He alleged that in Tantura on May 22-23, 1948, up to 200 prisoners and civilians were shot after the village had surrendered to Israeli forces.

On January 21, 2000, an Israeli tabloid newspaper published an article, based on Katz's thesis, in which several of his eyewitnesses were reinterviewed. The Palestinians largely confirmed their stories, but some of the Jewish ex-soldiers repudiated or modified what they had allegedly told the student. In the wake of the publicity, veterans from the Israeli army unit allegedly involved sued Katz for libel. The trial opened on December 13, 2000, with the prosecution's case centring on Katz's alleged misquotation - or even invention - of passages in his interview material.

But the case took a peculiar turn on the second day. Katz abruptly signed an "apology" that stated the massacre story was untrue. Explanations for this about-face were varied and confused: Katz was in poor health, he had been pressured by relatives, friends and possibly one of his lawyers.

Then within hours, Katz attempted to retract his retraction and resume the trial. The court refused. In December 2001, Katz once more sought permission to withdraw his "apology" and reopen the case. Again he failed.

Meanwhile, there was major academic fallout at Haifa. The award of Katz's MA degree was "suspended", and Ilan Pappe entered the picture. Pappe was already well known as one of the most radical of the youngish Israeli historians whose work challenged many cherished nationalist beliefs about the country's origins and ethos. He was not - as many commentators seem to believe - Katz's thesis supervisor: that was Druze historian Kais Firro.

But Pappe became the most prominent advocate and publicist for the massacre allegations. He charged Haifa University with "moral cowardice" for failing to support its embattled student. He further claimed to have subsequently faced censorship and harassment by university authorities. Pappe's international articles and lectures allegedly drew especial disapproval.

Firro, meanwhile, was less outspoken, believing the issue should remain academic rather than political.

Haifa appointed a committee of four experts to re-examine Katz's thesis, which announced that it had found major errors, although there was dispute over whether the committee was politically motivated. Katz was invited to revise and resubmit the thesis. The massively revised and lengthened version was completed by September 2002, correcting many misquotations and adding much new detail and verbatim transcriptions from his interviews. But it still argued that dozens, perhaps hundreds, of Tantura villagers had been massacred by Israeli forces.

The university then appointed five new examiners, whose names (and political leanings) were rapidly circulated on the internet. Their reports were startlingly divergent. Two gave clear pass marks of 83 and 85 per cent. Two, equally decisively, failed the thesis. The fifth awarded it a 74 per cent grade - not quite enough to pass. So Katz's work and its politically sensitive claims were rejected.

The focus of the dispute, though, was by now on Pappe. On November 19, 2001, he made a public international protest against Haifa's "shameful" decision to disqualify Katz's thesis. He was sharply critical of individuals at the university who had taken the "anti-Katz" side.

Meanwhile, those same individuals - at least some of whom disliked Pappe on political grounds - were moving against him. Conservative historian Yoav Gelber launched a series of criticisms, ranging from Pappe's historical methodologies to his alleged personal abuse of colleagues (and in the process used some pretty abusive language of his own).

Then Yossi Ben-Artzi, the dean of Haifa's faculty of humanities, lodged a formal complaint seeking Pappe's dismissal, claiming that the scholar had violated the institution's ethical code, adding, "his aim to defame, insult, humiliate, scorn and act in a lofty manner" was "damaging the good name and professional reputation of the university".

Pappe responded very publicly, writing a widely circulated letter to people around the world on May 14, 2002. In it, he denounced the forthcoming hearing as "a McCarthyist charade" and alleged that the university had decided to expel him to silence his support for both Katz and for an academic boycott of Israel. He concluded: "I ask those who are willing to do so to take this case as part of your overall appreciation of, and attitude to, the present situation in Israel. This should shed light also on the debate whether or not to boycott Israeli academia."

Petitions supporting Pappe circulated rapidly, many under the misapprehension that he had been sacked. Haifa's administration insisted they were following a proper complaints procedure under which Pappe was presumed innocent unless proven otherwise. Then the affair took another mysterious turn: Ben-Artzi's suit was dropped. Pappe's sympathisers naturally suspect that only international pressure had produced this result. He remains on the staff of the university.

The claim in the AUT's resolution that Pappe faces continuing "recriminations" cannot be dismissed. In May 2003, a conference he was set to run on the historiography of 1948 was cancelled by university authorities, in what Pappe saw as another act of political censorship.

Ben-Artzi, now rector of the university, is obviously a man of strong political views. Can one doubt that the nationalist rector would like to get rid of the troublesome left-wing historian? On the other hand, is it clear that the university has negated academic freedom or, in the AUT's words, "victimised academic staff and students who seek to research and discuss the history of the founding of the state of Israel"?

There is a fair amount of murk in the story and some starkly contrasting versions of events. I have read many hundreds of related articles, interviews and documents, talked in detail to many of those most closely involved. And I do not feel I know for sure what happened, either at Tantura or at Haifa.

So how can the members of the AUT, after just a few minutes' hasty debate, seem so confident that they do? And why have Israel's own left wing, anti-government academics not been consulted?Apart from Pappe, none, Arab or Jew, support the British action and many fear it will only make their own embattled position worse.

Stephen Howe is a former tutor in politics at Ruskin College, Oxford. This is an edited version of an article first published at openDemocracy.net