After that experience I have difficulty understanding anyone who equates Israel with apartheid South Africa. What I saw in the Hadassah Mt Scopus hospital was inconceivable in the South Africa where I spent most of my life, growing up and then working as a journalist who specialised in exposing apartheid. It didn't happen and it couldn't happen. Blacks and whites were strictly separated and blacks got the least and the worst. And this is only one slice of life. Buses, post offices, park benches, cinemas, everything, were segregated by law. No equation is possible.

That is what came to my mind as I read the Guardian's two-part report this week about Israel and apartheid. The writer, Chris McGreal, is an outstanding reporter. I admire his dispatches from Israel/Palestine. Day by day he honestly and correctly portrays the conflict. But these articles are disappointing. He has lost his way in thickets of information. He has been unable to untangle the confusion and complexities of group relations here. He is muddled in distinguishing between the situations of Israeli Arabs and West Bank Arabs and Jerusalem Arabs.

It is not that he is wholly wrong. Arabs suffer severe discrimination. Israel is in occupation of the West Bank and is responsible for oppressive and ugly actions. But he fails to explain the why and the wherefore. He had a choice in deciding how to decipher the situation. He could have adopted the approach of Heribert Adam and Kogila Moodley, well-known Canadian academics specialising in South Africa and the Middle East. In their book, Seeking Mandela, published last year, they say: "Although Israel and apartheid South Africa are often equated as 'colonial settler societies', we argue that the differences outweigh the similarities." They warn that the "simplistic assumption that the South African model readily lends itself to export may actually retard necessary new solutions by clinging to visions or processes of negotiation that may not work in another context". That assessment is surely far more relevant than quoting the debased views about South Africa and Israel of the late Hendrik Verwoerd, a father of apartheid, as McGreal has strangely done.

McGreal had to decide whether the glass is half-full or half-empty. His approach could have been that here is a tiny country which came into being, in the shadow of the Holocaust, less than 58 years ago. It has been under continual attack since the start and is still beset by enemies sworn to its destruction, whether Islamic Jihad and Hamas through suicide bombings, the Arab states through their refusal to recognise its existence, the recent "wipe-out" call by Iran's president, or the actions and declarations of a mixed bag of malevolent forces, anti-semites and semi-Jews. That induces a siege mentality among Israel's Jews. They fight to live and do not always do it pleasantly. They make horrible mistakes and inflict suffering on others. It is not secret. I do not know why Chris McGreal says the Israeli public is unaware of what is happening: newspapers publish the details in profusion, provoking discussion and action.

Yes, racism does exist in Israel - directed against Arabs, and also among Jews. Amir Peretz, new leader of the Labour party, is said to be having problems with western-born Ashkenazi voters because he is Moroccan-born and Sephardic. An explanation offered for the police violence in clearing the Amona outpost last week was the antagonism between the protesting young people, who were mainly religious Ashkenazi, and the police, who were a mixture of Moroccan and Russian immigrant stock, Bedouin and Druze.

Is Israel so different from other countries that struggle to come to terms with their minority groups? Why depict this country as a chamber of horrors like no other in the world?

The glass is indeed half-full. In South Africa, change for the better was simply not possible: the apartheid system had to be eradicated. In contrast, change is possible in Israel. An accusation by a member of the Knesset, Ahmed Tibi, who is Arab, that the central Bank of Israel had a discriminatory employment policy with no Arabs among its 800 staffers, drew the assurance from the bank's then governor that tenders would be advertised in the Arab-language press. He added: "Bank of Israel hires according to criteria of merit, and ignores differences in religion, sex, race or nationality." Tibi also complained that the state monopoly Israel Electric did not employ Arabs; a start has since been made with the hiring of six Arabs. There is continual progress: the evidence is there if you want to see it. The first Arab was appointed to the high court of justice two years ago. Last year, for the first time, an Arab was appointed director-general of a government ministry.

McGreal notes that inside Israel, 93% of the land is reserved for Jews while South Africa's whites kept 87% of the land for themselves. Thus Israel and apartheid South Africa are the same. But the QED is not as straightforward as his citing of these figures would have us believe. In law, land in Israel is open to everyone but, yes, in practice, through legal stratagems, 93% of the land has been only for Jews. This, however, has been breached by the Arab Ka'adan family: in a 10-year legal struggle, they have established their right to buy land and build a home in the "Jewish" community settlement of Katzir in northern Israel. The high court of justice has given a precedent-setting decision that the state cannot discriminate on the basis of religion or nationality when allocating state land to Israeli citizens. The case has dragged on but final success is in sight. Other court actions are underway. Land exemplifies both the negative and positive aspects of the lives of Israel's Arabs: it conveys the discrimination - and the movement towards change; slow, slow, but underway.

On education, McGreal states that separate and unequal education systems were a central part of the apartheid regime's strategy to limit black children to manual and service jobs - something I observed firsthand and fought against in South Africa. But I have to question his reference to what he says is the current belief among Arab parents that their children's schools are deliberately starved of state resources so that Arabs will be doomed to lesser jobs. Every government school, whether Jewish or Arab, gets identical funding; differences, and hence resources, arise through what parents pay and what local authorities pay (most local authorities in Israel are in poor financial shape; Arab local authorities are even worse off with problems in collecting local property taxes). The Jewish schools are Jewish day schools. The Arab schools are Muslim and use Arabic, which is an official language in Israel. There is no bar to Arabs attending Jewish schools, and some do.

I am also puzzled by the health ministry figures that McGreal has chosen to use about state spending on development of health facilities in Arab areas (the clear implication being that Arabs are starved of health care). Contrary to the picture painted, health is a visible indicator of the differences between apartheid South Africa and Israel. In South Africa, the infant mortality rate (IMR) in 1985 was 78 per 1,000 live births. Among colour groups: whites 12, Asians 20, coloureds 60, blacks 94 to 150. In Israel, in the 1950s, the IMR among Muslims was 60.6 and among Jews 38.8. Major improvements occurred in health care during the 1990s and by 2001 the IMR among Arabs was 7.6 (Muslims 8.2, Christians 2.6, Druze 4.7). Among Jews, 4.1. According to the health ministry, the higher Muslim figure was due mainly to genetic defects as a result of marriages between close relatives; poverty is also a factor. Other countries in 2000: Switzerland, 8.2, and 12.3 for Turks living there; United States, whites 8.5, blacks 21.3.

He is also mistaken in saying that Arabs have been singled out for discrimination in getting reduced child allowances. They are the same as Jewish ultra-Orthodox families. These two groups have the largest number of children and have suffered equally from cutbacks in allowances, especially for the fifth child and beyond.

Here in Jerusalem on Monday, I watched the BBC's Auschwitz on television. The episode dealt with French collaboration in delivering Jews to the Nazis for destruction, and how British policemen on Guernsey handed over three Jewish women. It was a reminder, if any be needed, of why Israel exists: to fulfil the centuries-old dream of a homeland for Jews and as a sanctuary for Jews. It's not a perfect society. It struggles to find itself as a Jewish state (with no consensus about what that means), and it struggles to evolve as a democratic society with full rights for minorities. It deserves criticism for its flaws and mistakes. It also merits sympathy and support in facing unfounded attack.

· Benjamin Pogrund was born in South Africa and was deputy editor of the Rand Daily Mail in Johannesburg. He is the author of books on Robert Sobukwe, Nelson Mandela and the press under apartheid. He has lived in Israel for more than eight years and is founder of Yakar's Centre for Social Concern in Jerusalem, which encourages dialogue across political and ethnic lines.