Mike Steketee, National Affairs Editor – Downer's achievements as our longest serving foreign minister aren't all he claims and must be balanced against some calamitous mistakes

Savouring his record as Australia's longest serving foreign minister, Alexander Downer offers as his greatest achievement the creation of a free and independent East Timor.

Funny, then, that this is not quite the result that Downer and John Howard had in mind at the time. In fact, Hugh White, who as a Defence Department deputy secretary was involved in Australia's response during those years, says the outcome in the form of the vote for independence at the end of 1999 "differed in every respect from the government's objectives at the start of the year".

Call it characteristic Downer chutzpah, somewhat similar to taking a paid job as UN special envoy to Cyprus after spending most of the past decade bagging the UN as worse than useless.

Australia's intention had been for East Timor to stay part of Indonesia. Howard made that clear in the letter he sent to then Indonesian president B.J. Habibie, a letter that Downer says he initiated.

It suggested a process that would "allow time to convince the East Timorese of the benefits of autonomy within the Indonesian republic", followed by an act of self-determination. Like every government before and after, whether Labor or Coalition, the Howard government placed much higher priority on a good relationship with Indonesia than on the fate of a few hundred thousand East Timorese.

There was no enthusiasm for a new and potentially unstable mini-state on Australia's doorstep.

But the mercurial Habibie opted instead for a ballot offering East Timorese a choice between autonomy under Indonesian rule and Full independence. From there, events moved largely out of Australia's control.

So keen was Downer to keep the Indonesians on side that he denied Jakarta was orchestrating the violence in the months leading up to the vote. "Rogue elements" might be involved, he said, but "I do accept the Indonesian government's word for it that it's not official Indonesian policy".

Last week a three-year joint inquiry by the Indonesian and East Timorese governments confirmed what Australian intelligence was telling Canberra in 1999: that the Indonesian military, together with police and civilian authorities, organised and funded the violence that left 1500 people dead and destroyed significant parts of the country. Downer's response? He had known that elements of the Indonesian military were behind the violence but he didn't think Habibie had sanctioned it.

Writing in a recent edition of the journal Security Challenges, White, now professor of strategic studies at the Australian National University, says Downer's comments in 1999 went "against the clear weight of intelligence reporting and assessment", and adds tactfully: "This perhaps reflected a desire not to damage relations with Indonesia and especially with TNI (the Indonesian armed forces)."

But at what cost? In early 1999, before the vote at the end of August, US assistant secretary of state Stanley Roth wanted a concerted international push for a peacekeeping force. Then Department of Foreign Affairs and Trade secretary Ashton Calvert argued such a course would be counterproductive.

White says it is uncertain whether Howard pushed for an international peacekeeping force when he met Habibie in April and, if so, how hard. He adds that there was strong resistance from Indonesia to such an idea. But he concludes: "It may well be that by not pushing harder at this time, both directly with Habibie and through others like the UN and the US, we missed the last best chance to avoid the disasters of September (the post-ballot violence)."

The initiative Howard took after the ballot for an Australian-led international force succeeded in restoring order and Australia maintains an important presence in East Timor today. But White's point is that it turned out very differently to what the government had intended. The aim had been to avoid sending a large Australian military force to East Timor. The belated intervention severely strained relations with Indonesia and the Indonesian army. Hopefully, even if its creation was more by accident than Australian design, East Timor will be able to develop beyond a fragile state with Australian assistance.

Downer is in New York, sizing up his job as UN special envoy to Cyprus. Presumably, all is forgiven, including his lecture to the UN General Assembly two years ago: "Effective international action on the great global challenges of our time requires more than resolutions in the (UN)... It requires proactive policy, not political posturing and personal abuse from this podium."

Of course, Downer has a point about the UN's lack of effectiveness. Hopefully, he will find a resolution to the Cyprus problem that has eluded the Greeks, the Turks and the UN for the past 34 years. But it is a pity the Howard government did not take more notice of the UN when it was asking for more time for its weapons inspectors, rather than barging into Iraq with the US and Britain.

Downer maintained his confidence about finding weapons of mass destruction months after the invasion and when it had become clear to many others that none existed. When Downer was looking for a scapegoat for AWB paying huge bribes to the tyrant we went to war against and doing so under the noses of the Australian government, he picked the UN.

Downer has achievements to his name as foreign minister, including a peace agreement in Bougainville and the regional assistance mission to Solomon Islands.

He contributed to what diplomats call the international architecture, gaining Australian access to the East Asia group, initiating negotiations on free trade agreements with Japan and China, and coming up with a trilateral strategic dialogue with Japan and the US.

But he also was involved in some calamitous mistakes. And we could have done without the hubris.