Two decades earlier the island's population of pipistrelles had been healthy. A few scientists had watched the species' decline with concern, until, after the million or more years that it had played a part in keeping the ecological balance of the island, they could see that without action its demise was imminent. They had done their best to warn the federal government about the looming catastrophe, but they might as well have been talking to a brick wall. The bureaucrats and politicians prevaricated for three years, until it was too late.

Nothing effective was done to help the bats. Indeed, except for those watching scientists, few seemed to give a thought to the passing of the species, nor what it might mean for Christmas Island or our country.

The pipistrelle's extinction was painful for me. In an attempt to avert it I met Peter Garrett, then the environment minister, and warned him of the impending loss. I had brought offers of assistance and expertise from the Australian Mammal Society to his attention. The society was confident the species could be saved - at a cost of perhaps only a few hundred thousand dollars. But Garrett was convinced by the orthodoxy that ecosystems rather than species should be the focus of the national conservation effort, and I got the message that nothing would be done. Saving the bat wasn't an impossible mission. It's just that the government and the people of Australia - one of the richest countries on earth - decided it wasn't worth doing.

What really shook me was that it was the first extinction of a mammal in Australia for 60 years - and the first in my lifetime. My original professional expertise lies in mammalogy and palaeontology, and before the pipistrelle's demise I believed the worst of Australia's extinction crisis was behind us - that somehow my generation was wiser and more caring, and would not tolerate any more losses of Australia's unique mammals. It's now clear that those 60 years were a lull in the storm, and that the pipistrelle's demise marked the beginning of a new extinction wave.

Australia's first extinction wave began almost as soon as the First Fleeters stepped ashore, and by the 1940s it had carried away 10 per cent of the continent's mammal species. In 1791, a convict wrote about the white-footed rabbit rat, saying it was a pest in the colony's food stores. The soft-furred, grey and white kitten-sized creature was arguably the most beautiful of Australia's 70-odd native rodent species, yet it was destined to be one of the earliest victims of European settlement. Two hundred years ago it could be found in woodlands from near Brisbane to Adelaide, but the last record of it dates to the 1850s.

The thylacine and the toolache wallaby were the largest creatures to succumb in the first extinction wave. These extinctions were, however, atypical. Indeed, one of the most astonishing aspects of the first extinction wave was that its victims included what had been the most abundant and seemingly secure mammals in Australia.

The causes of these extraordinary extinctions were varied. The cessation of Aboriginal burning doubtless had its effect, and until the 1930s bounties were paid by many state governments for the scalps of now-extinct creatures. But the depredations of foxes (which were spreading quickly by the early 20th century) and feral cats, and the wholesale destruction of native vegetation by livestock and rabbits, must have been important causes. While the causes are disputed, the effect of the first extinction wave is clear: it gutted the biodiversity of the drier parts of the continent, and few native mammals larger than a rat and smaller than a kangaroo can be found on Australia's inland plains today. It's the absence of such species - the so-called critical-weight-range mammals (which weigh between 500 grams and 5 kilograms), which were once among the most abundant of creatures - that has led me to characterise the national parks of Australia's southern inland as ''marsupial ghost towns''.

The gathering second extinction wave is now mopping up the few surviving medium-sized mammals in Australia's south and inland. It's not difficult to predict what will be the next to become extinct, for, like the pipistrelle, their decline has been charted for years. There are 15 frogs, 16 reptiles, 44 birds, 35 mammals and 531 plants on Australia's endangered species list, and among those closest to the brink are three mammals: the central rock rat, the bridled nailtail wallaby and the numbat. All hang by a thread, and next to nothing effective is being done to halt their slide into oblivion.

The most dismaying aspect of the second extinction wave is that it is emptying vast swathes of the continent that were untouched by the first wave. Australia's Top End and Kimberley were, until recently, a paradise for medium-sized mammals, among them a close relative of the white-footed rabbit rat. The last two decades have resulted in this fauna all but exterminated in the Top End, even in our most-valued and best-resourced national parks.

Perhaps it is excusable that Australians are unaware of the extinctions now occurring in distant places such as Arnhem Land and other regions of our far north. But astonishingly, we also seem blind to the perils facing species much closer to home - for example, the sand flathead of Port Phillip Bay. A fish familiar to every Melburnian who has ever dangled a line, its population has declined by 97 per cent over the past decade.

Why should the extinction of Australian organisms concern us? The answer is almost precisely the same as to the question of why human rights are important, even when they concern people we'll never meet. First and foremost, it is a matter of values. The demise of a bat may not weigh greatly in the balance of human wellbeing, but it speaks volumes about the human soul.

As with human rights, extinctions beg the question of where we draw the line. If we can stand by as a species of bat is snuffed out, then why not other species as well? Can we really expect poor Indian villagers to heed our pleas to conserve the tigers that menace their livestock if we do nothing to prevent the extinction of Australian species? As with the question of torture, to open the door to the practice of extinction is to contemplate the horrific becoming routine.

At the heart of this nation's efforts to save its endangered species is a register of subspecies, species and ecological communities threatened with extinction. By law, each entity included on the list should have a detailed recovery plan written for it, which when implemented should save it from extinction. These plans classify species on a sliding scale - from vulnerable to critically endangered or extinct. The federal legislation governing these plans states: ''Recovery plans are binding on the Australian government - once a recovery plan is in place, Australian government agencies must act in accordance with that plan.''

What a wonderful reassurance. It's a pity, then, the system underpinning the promise is rotten. By their fruit ye shall know them: since the legislation mandating action plans was enacted in 1992, only a single vertebrate species has become so abundant as to merit being taken off the threatened species register. But saltwater crocs are atypical of Australia's endangered species in that the threat they faced was simple: when the shooting for skins was stopped, the species recovered.

Why are we failing so abjectly in protecting our threatened species? The pitifully slow rate at which recovery plans are being drafted is one factor. In NSW, for example, in the past 20 years, recovery plans have been completed for only around 10 per cent of all species listed as vulnerable to extinction. Things get worse. In 2006, the federal government excused itself from the obligation to draft plans for species listed as vulnerable to extinction. As a result, if the Minister for the Environment decides not to draft a plan, then it simply isn't done. And even if a plan is completed, there's no guarantee it will receive funding.

Why are action plans so often failing to help species recover? The glacially slow development of the plans, along with the lack of obligation to fund and report back on them, are clearly impediments. There are other problems as well. Some plans do not describe how species might be saved. Instead, they often stated that more money is required for research before appropriate action is taken.

Such is the depth of public ignorance about Australia's extinction crisis that most people are unaware it is occurring, while those who do know of it commonly believe our national parks and reserves are safe places for threatened species. In fact the second extinction wave is in full swing, and it's emptying our national parks and wildlife reserves as ruthlessly as other landscapes. This is disturbing. National parks exist explicitly to conserve biodiversity, and their failure to do so is a failure both of government policy and our collective will to protect our natural heritage.

The problem lies not with the parks' staff, who are often dedicated and skilled at their work. Nor does it lie solely with budgets, although more funding rather than more cuts would always be welcome. Instead, the difficulties are at least threefold. First, the problem stems from the delusion that the simple act of proclaiming a national park or nature reserve will result in the protection of biodiversity. Parks must be proclaimed and effectively managed if biodiversity is to be protected.

Second, the various government agencies responsible for biodiversity protection have allowed their scientific capacity to erode to the point where it's hard to be sure how many individuals of most endangered species survive; and third, the attempt to save endangered species involves risks that bureaucracies are increasingly unwilling to take.

The first duty of the bureaucrat these days seems to be to protect their minister from criticism. Thus it often seems preferable to let a species die out quietly, seemingly a victim of natural change, than to institute a recovery program that carries a risk of failure, however small.

Australian politics, and the bureaucracy that supports it, is failing in one of its most fundamental obligations to future generations: the conservation of our natural heritage. The times also suit cynical self-interest. Cash-starved state governments, ever more desperate for income and political support, are rolling back even the inadequate protections that presently exist, and economic pressures are making it difficult for not-for-profit organisations that focus on nature protection to make ends meet.

What to do? As this saga of ignorance, folly and malice unfolds, it has become clear those working outside government have a crucial role to play in conserving our biodiversity. I believe it is action by the private and not-for-profit sectors, working with government, that holds the key to protecting our endangered species in a competent and affordable manner. Australians need to take a look at ourselves.

This is an edited extract from Australia's New Extinction Crisis by Tim Flannery, published in the latest Quarterly Essay.