Damien Kingsbury, Indonesia expert and Associate Professor of International and Political Studies at Deakin University, writes:

Australia's move to reach a broad-ranging agreement with Indonesia over security co-operation is a logical outcome of the strengthening of ties between the two countries in the wake of growing joint counter-terrorism measures and Australia's post-tsunami emergency and financial assistance. It is, in a large sense, a renewal of Australia's security treaty with Indonesia reached by the Keating government in 1995, scrapped in 1999 in the wake of East Timor's independence vote and destruction.

The main drivers for this renewed treaty are Indonesia's desire to move closer to Western countries, especially the US, with Australia seen as a gateway to that wider relationship. Indonesia's relationship with the US administration has been steadily improving, especially given the perception by Bush and Company of the role that Indonesia can play in its anti-terrorism struggle. This agreement will now assist the US administration in getting the more reluctant Congress on side, especially on issues of military to military co-operation and arms supplies.

Australia's Department of Foreign Affairs and Trade also has a long history of seeking closer ties to Indonesia, very often at the expense of the wider concern of Australian citizens over human rights and related issues.

The new agreement is today reported to contain a clause which stipulates that Australia will not interfere in the internal affairs of Indonesia and will respect its territorial sovereignty. At one level, such a clause is a conventional recognition of the sovereign independence of another state. Yet such clauses are also rare in bilateral agreements, as sovereign respect is assumed as a given.

In the case of Australia and Indonesia, such a clause reflects lingering doubts over Australia's long term intentions, especially for the now divided province of Papua. There are some in Jakarta, especially in the legislature's foreign affairs and defence committee, who believe that Australia is intent on dismembering Indonesia, following its intervention in East Timor in 1999. Such a clause is intended to allay such fears.

However, there will also be many in Indonesia who will view such a clause as limiting Australia's capacity to speak critically on particular issues within Indonesia, should such concerns arise. This has the potential to raise objections to any Australian criticism or commentary that is not perceived as supportive, and may be held as applying not just to the government but to the media and non-government organisations.

There has been a long history of Indonesian sensitivity to Australian criticism, especially by the Australian media, and to claims of interference by some NGOs, especially on human rights issues. The inclusion of a non-interference clause, then, could open the way for the Indonesian government to request official pressure on the Australian media to curtail their Indonesia-focused observations, and for NGOs to limit their activities in relation to that country.