The complete withdrawal of the Yugoslav army from Kosovo last night has brought to a close another chapter in the Balkan wars. In purely strategic terms, President Slobodan Milosevic's defeat is total. He has retained more of his military machine than NATO would like to admit and, of course, he managed to save his skin as well, at least for the moment.

However, almost regardless of what happens in the years to come, it is hard to see how the Belgrade ruler or any of his potential successors would ever have any say over Kosovo.

And yet, in moral terms, the Kosovo war ended in the same inconclusive manner as did the conflicts in Slovenia, Croatia and Bosnia earlier this decade: the chief aggressor was pushed back but not punished; the victims have been helped, but their sacrifice hardly redeemed.

Wherever NATO troops marched they discovered medieval torture chambers, mass graves and randomly-scattered human remains. Meanwhile those who ran this atrocious human abattoir are now sipping drinks in Belgrade's cafes.

It is tempting to believe that the horrors were perpetrated by Serb paramilitary formations which escaped anyone's control, aided by local madmen. To a certain extent, this was the story in Croatia and Bosnia during the early 1990s, when killings were committed chiefly by Serbs who resided in these republics, and where grabbing land and settling old economic and social grievances were just as important for the Serbs as the destruction of their ethnic enemies.

But the Kosovo episode is more horrific than that.

In terms of sheer numbers, the Yugoslav killing machine still cannot be compared with the Holocaust perpetrated by the Nazis. However, the inspiration was the same, and the technique almost identical.

For the first time since Yugoslavia collapsed, the West has concrete evidence of organised and systematic murder, not merely inspired by Belgrade - as was the case in the other Balkan wars this decade - but actually conducted from the Yugoslav capital. The methodical collection of identity papers, the precise destruction of one ethnic Albanian village after another, the use of local trains to transport those evicted and the organised structure for disposing of the victims' bodies are reminiscent of Nazi Germany during the second World War.

And, to make matters even worse, so is the reaction of the bulk of Yugoslavia's population.

Patriarch Pavle, the head of Serbia's Orthodox Church, called last week for Mr Milosevic's resignation. It was a daring act with potentially far-reaching consequences: the Belgrade dictator is an old communist who never goes to church, but he cannot ignore the voice of the Primate, who embodies the essence of Serb nationalism.

Yet at no point did the Patriarch even allude to the horrors which were committed against the ethnic Albanians who were, after all, Yugoslavia's citizens; his criticism of Mr Milosevic was based on the simple fact that he had lost a war, and had failed to protect the holy places of the Orthodox faith in Kosovo.

Nor are any opposition leaders in Belgrade bothered with this wholesale murder; they prefer instead to criticise Yugoslavia's dire economic situation.

Apart from a few isolated intellectuals, the people of Yugoslavia are suffering from collective amnesia: rather like the bulk of ordinary Germans during the 1940s, they know nothing, have seen nothing and have nothing to answer for.

To a large extent this outcome was inevitable. It was known from the start that NATO's air offensive would not be able to prevent the atrocities; the best the West could hope for was that the atrocities would be isolated, and short-lived. They were neither: the murder was well-organised and lasted for 75 long days.

The decision not to use ground forces, thereby sparing the Western military more casualties but prolonging the Albanians' agony, will be debated in years to come by historians, just as the decision not to bomb the Nazi extermination camps during the second World War is still hotly disputed to this day.

But one fact is already obvious. By opting for a negotiated solution which ultimately entailed the staggered entry of Western forces as Yugoslav troops withdrew from Kosovo, NATO not only accepted that it was impotent to prevent the massacres but also tacitly admitted that most of the criminals responsible for this wholesale slaughter would evade justice, at least in the short term.

Those in the West who argued against the war should now accept that this campaign was essential for the preservation of Europe's humanity. But those Western leaders who conducted the campaign, although vindicated in their approach, should also exercise humility by admitting that, ultimately, Europe failed to prevent another racial mass murder on its doorstep.

The war had to be, and was, won. However, the horrible deed was committed.

Yet not all the news is grim. The bulk of the atrocities in Bosnia took place before the International War Crimes Tribunal was established. The tribunal's task of collecting information was therefore much more difficult.

In Kosovo, however, evidence has been accumulated since the terror began in February last year. This task is now supported by many forensic teams, which have the benefit of starting work when most of the evidence is still physically available.

Furthermore, during the Bosnian conflict Western governments treated the international tribunal with ambivalence, mainly because they were nervous about the legal principles which were being established.

This official reticence has disappeared: the tribunal knew of many massacre sites weeks ago, through information provided by Western intelligence agencies. A new European legal regime has therefore been created; the tribunal has become a permanent feature of our lives, a bulwark against future atrocities.

Of course this does not mean that justice will be done: most of the perpetrators of the current massacres will never have to answer for their deeds. But even here, there are grounds for optimism.

Those indicted for the crimes will never be able to travel. With every political change which will take place in Belgrade they will fear arrest, and anyone who takes over from Mr Milosevic will spare some of them while extraditing others.

Indirectly, therefore, the war crimes tribunal has become part and parcel of Yugoslavia's own life. The citizens of Yugoslavia will continue with their own self-denying amnesia, as people usually do when it comes to their own crimes. But the long shadow of the tribunal will continue to hang over them for years to come.

Justice at an international level has always been an incremental process. The sole source of satisfaction in Kosovo is that Europe has made a step forward, despite all the horrors.

Jonathan Eyal is director of studies at the Royal United Services Institute in London.