I remember the boys dressed in army surplus, the girls in hessian, silhouettes framed in beach shanties, staring across an abyss. You were not meant to talk about them. They were not counted in the census, unlike the sheep, and anyway were dirty and feckless and dying off.

You were not meant to disturb the surface of our great southern idyll, sun-kissed and God-blessed, in circumstances that might raise questions of race. At high school, I studied a celebrated historian, Russel Ward, who wrote: "We are civilised and they are not." They were the first Australians. At least he mentioned them. Other textbooks simply left them out.

Today, almost everything has changed and has not changed. For many Aboriginal people, who value healing, Prime Minister Kevin Rudd's apology last year was important. They and their white allies had worked tirelessly for the mere word to be uttered. The resistance was formidable; white supremacist politicians, journalists and academics damned the "black armband version of our history". And when Rudd finally said it, the Sydney Morning Herald described the apology as "a piece of political wreckage" that the "government has moved quickly to clear away . . . in a way that responds to some of its supporters' emotional needs".

Australia's apartheid

There is to be no compensation for those thousands of Aborigines wrenched from their families as children, known as the stolen generation. And the previous, openly racist government's "intervention" into Aboriginal lands in the Northern Territory is being consolidated. In 2007, on the pretext that Aboriginal children were being sexually abused in "unthinkable numbers", the government of John Howard suspended the Racial Discrimination Act and sent the army and "business managers" to take over black communities.

Within a year, barely reported statistics proved how bogus it all was. Out of 7,433 children examined by doctors, at most four possible cases of sexual abuse were identified. The Australian Crimes Commission found no evidence of paedophile rings. What it found, it already knew: poverty and sickness on the scale of Africa and India.

Since Rudd's apology, Aboriginal poverty indicators have gone backwards. His "Closing the Gap" programme is a grim joke, having produced not a single new housing project.

An undeclared agenda comes straight from Australia's colonial past: a land-grab combined with an almost prurient need to control, harass and blame a people who have refused to die off, whose genius is their understanding of an ancient land that still perplexes and threatens white authority. Whenever Canberra's politicians want to look "tough", they give the Aborigines a good kicking: it is a ritual as sacred as Don Bradman worship or Anzac Day.

The indigenous affairs minister, Jenny Macklin, has decreed that unless certain communities hand over their precious freehold leases, they will be denied basic services. The Northern Territory contains abundant mineral wealth, such as uranium, and has long been eyed by multinationals as a lucrative radioactive waste dump. The blacks are in the way, yet again: so it is time for the usual feigned innocence. Rudd has said his government "doesn't have a clear idea of what's happening on the ground" in Aboriginal Australia. What? The learned studies pour forth as if the sorcerer's apprentice is loose.

One example: the rate of incarceration of black Australians is five times that of black South Africans during apartheid. Western Australia imprisons Aboriginal men at eight times the apartheid figure, an Aussie world record.

On 16 November, a 12-year-old Aboriginal boy appeared in court charged with receiving a Freddo Frog chocolate bar from a friend who had allegedly taken it from a supermarket. Only the international headlines forced the police to drop the case. Two-thirds of Aboriginal children who have contact with the police are jailed; two-thirds of white children are cautioned. A young Aboriginal man was jailed for a year for stealing £12 worth of biscuits and soft drink.

A mattress in the desert

In my lifetime, Australia has become one of the most culturally diverse places on earth, and it has happened peacefully, by and large. This proud achievement fades when you drive into a country town and pass the funerals of native people, many of them young, who take their own lives. The whispering in Antipodean hearts is race. The navy is sent against leaking boats filled with refugees, Tamils and Afghans, and if they cannot be dumped behind razor wire somewhere in Indonesia, they are isolated on Christmas Island, which, for the purpose, has been "excised" from the Australian map by a legal sleight of hand. How clever.

While I have been in Australia, Irene Khan, Amnesty's secretary general, has been travelling through the vast outback region known as Utopia. The roads are dirt; water often trickles from a single standpipe. She saw children, their eyes streaming and coughs hacking. She met Elsie, who sleeps on a mattress in the desert, yet pays rent to the government. Shocking, she says.

There is currently a liberal clarion call for a bill of rights, and the republican movement is stirring again. These debates are meaningless until white Australia summons the moral and political imagination to offer its first people a genuine treaty, as well as universal land rights and a proper share of resources. And respect. Only then will this fortunate society earn the respect it so often craves by other means.

On 4 November, John Pilger received the Sydney Peace Prize, Australia's international human rights award. "A Secret Country", his history of Australia, published 20 years ago, remains in print (Vintage, £10.99)

www.johnpilger.com

Next week: Mehdi Hasan