Asian nations, not surprisingly, were affronted. Malaysian politicians accused Mr Howard of being racist and patronising, while an Indonesian political analyst, Salim Said, said: "Howard is like a 19th century European standing on a beach and thinking he will have to watch out for the little brown uncivilised neighbours that lie to the north."
It has not gone down too well at home either. But Mr Howard's "doctrine" reflects the extent to which, in the wake of East Timor, Australia's view of its place in the world has been turned upside-down.
Since the small territory across the Timor Sea blew up nearly a month ago, Australia has been engaged in its most agonised bout of soul-searching for decades. Less than a week into the Australian-led peacekeeping operation, one thing is already clear: East Timor has forced a complete reappraisal of the country's foreign and defence policy.
A good relationship with Indonesia has long been a central plank of that policy, mainly out of geographical necessity. Indonesia is Australia's closest neighbour in south-east Asia. For Australia, a sparsely-populated, affluent nation, the proximity of a large, unstable, predominantly Muslim third world country is a source of deep unease.
Events in East Timor have intensified that anxiety. And with other parts of Indonesia expressing nationalist aspirations, the spectre has been raised of a Balkans-style disintegration - which could seriously threaten strategic military and trade routes from Europe and the Middle East through to south-east Asia and Japan.
Hitherto, Australia's dealings with Indonesia have been characterised by a pragmatism bordering on the cynical. It was the only Western country to recognise Indonesia's annexation of East Timor in 1975, and one of the few to have sponsored joint military training programmes.
Relations are at the lowest point for nearly 40 years and Australia's leading role in Interfet, the multi-national force in East Timor, is causing distrust further afield in the region. As Michelle Grattan, a political commentator with the Sydney Morning Herald says: "Australia's relations with Indonesia, and possibly its wider Asian relations, are about to be rewritten for a generation."
In East Timor, Australia is in a peculiarly awkward position. While British military sources have suggested that its troops are being excessively restrained, the Thais - in deputy command of the force - have accused them of acting too aggressively. Important bilateral trade links are likely to be affected. On Friday Indonesia threatened to cancel Australian wheat imports. Cotton and sugar imports are also in jeopardy.
East Timor has confronted Australia with two painful realities. One, that Australia cannot count on US support in regional trouble spots. Two, that Australian defence spending - 1.7 per cent of gross national product, compared to, say, 2.9 per cent in Britain - will have to rise.
Gerard Henderson, executive director of the Sydney Institute, a conservative think-tank, says that events in East Timor show that there are "no certainties in international politics". He adds: "This should send a special message to an isolated nation of a mere 19 million people."