It is hardly novel that a politician looking back at the glory days of office will want to ensure that their political legacy looks as positive as possible. And for whatever faults one might find with John Howard’s period as prime minister, he was a politically-successful prime minister.
One wonders, then, why Howard finds it necessary to create a palpable fiction over his commitment to East Timor's independence, which he claimed was both inevitable and that he would go along with it. Similarly, one wonders why a journalist of Paul Kelly's stature would participate in the peddling of the fiction that "the Howard government decided in early 1999 to work for East Timor's independence", given evidence to the opposite is both overwhelming and freely available.
Howard's claim is contained in Paul Kelly’s book The March of Patriots -- the Struggle for Modern Australia, the subject of a self-authored puff piece  in The Weekend Australian. In short, Howard did not "work for east Timor’s independence". In fact, both his words and actions were contrary to this outcome.
By late 1998, Indonesia had already been involved in discussions with Portugal and the UN about moving towards some sort of resolution to the East Timor issue, and the Indonesian army had begun forming its anti-independence militias from that time. Howard's letter to Indonesia's President Habibie in December 1998 suggesting a protracted process of resolution was intended to ensure that Australia was no longer seen to be unquestioningly endorsing East Timor's incorporation into Indonesia at a time when Indonesian's no longer held such a view.
Howard’s foreign minister, Alexander Downer, publically accepted Indonesia's patently false denials about the militias, despite intelligence briefs to the contrary. In a discussion between DFAT secretary Ashton Calvert and senior US envoy Stanley Roth, Roth said that a full-scale peace-keeping operation in East Timor was necessary. Calvert, acting on government orders, refused. Roth later said Australia's policy of keeping the peace-keeping option at "arms length was essentially defeatist".
Howard also opposed having official Australian observers to the ballot, and only accepted the need for a small parliamentary delegation at the last moment, and after the creation of a politically independent Australian NGO observer group.
Australian Defence Forces were similarly told not to prepare for involvement in East Timor, including no logistic support for the ballot or to send military observers. It did, however, plan to extract Australian civilians if and when the situation deteriorated. Yet just two weeks ahead of the ballot, Downer told Australian observers in the courtyard of Dili’s Resende Inn that they should not expect assistance if the security situation deteriorated further. The message was clear: do not stay. That was the same message being sent at that time by the militias, who wanted not witnesses to their carnage.
At this time, the Australian government was acting against -- and denying the content of -- a flood if since leaked intelligence showing the Indonesian army was working to derail the ballot. The Howard government’s position on East Timor was, in public that it should remain as part of Indonesia, and in private that it would do nothing to hinder that outcome.
In that Australia sent an intervention force, the Howard government did not even give the order to prepare until 7 September -- more than a week after the ballot, and the force was immediately faced with equipment shortfalls due to this lack of planning.
Ultimately Australia was pushed into leading INTERFET by the US, which acted as guarantor for Indonesia's acquiescence. To suggest, as Howard has done, that he secretly supported East Timor's independence can only be understood as true if such a secret was not only kept from the public, but also government ministers, the most senior government officials and the Australian Defence Force that was ultimately required to cobble together an intervention capacity.
Australia's intervention in East Timor was a great achievement, if too late to stop a slaughter. But it followed the outrage of the Australian people, not some "secret" agenda of the then prime minister.