The recent visit of Indonesian Foreign Minister Hassan Wirajuda to Australia on Feb. 7 aimed to re-enforce the framework for security cooperation between Australia and Indonesia, known as the Lombok Treaty. A draft of this agreement was signed on Nov. 13, 2006, in Mataram by both governments, and the parliaments of both countries have approved the treaty.

The Lombok Treaty covers several areas. There are some major concerns in human rights circles over various parts of the agreement.

Article 2, item 2, which refers to "non-interference in the internal affairs of one another" is broad enough for each party to translate it as they wish. Yet it is important that human rights and democracy are not regarded as internal affairs. Human rights and democracy are global issues, relevant to the entire international community. It is the obligation of each nation, particularly those who are members of the UN, to uphold and spread the values of human rights and democracy.

The label of "separatists" has been used by Indonesian authorities to persecute people who criticize the government’s human rights abuses.

There remains a very real concern that the Indonesian government is still persecuting people in West Papua for being "separatists".

The article was included in the agreement in the hope of avoiding a repeat of the tensions which occurred in Timor Leste, where the Howard government sent troops after post-referendum violence.

This was regarded as a betrayal of Australian promises of support for Indonesian sovereignty in the then-Indonesian province. Could this happen again over West Papua? What about political refugees seeking asylum in Australia from various provinces? The article is meant to allay Indonesian fears.

In the first section of Article 3, the Lombok Treaty deals with "the long term mutual benefit of the closest professional cooperation between… Defense Forces".

To improve the Indonesian Military’s (TNI) professionalism, the Australian government should not only focus on joint military exercises (which have been criticized by several Australian and Indonesian human rights groups) but rather on improving the TNI’s management of the defense budget.

During his speech on Feb. 7, Australian Foreign Minister Stephen Smith mentioned the possibility of renewing the MOU on counter-terrorism cooperation, which has helped to eliminate terrorist organizations in Indonesia.

However, counter-terrorism exercises between Indonesia’s controversial special forces, Kopasus, and Australia’s Special Air Service Regiment, could cause problems for Kevin Rudd’s new government, given the role of Kopasus in conflict areas such as Papua.

The Intelligence Cooperation section of Article 3 needs to be clarified. Indonesian authorities often use the intelligence agency to monitor the activities of human rights and democracy activists.

Under Article 3’s section on the Proliferation of Weapons of Mass Destruction comments need to be made concerning item 17, which encourages "strengthening bilateral nuclear cooperation for peaceful purposes". The Indonesian government has been struggling to find some solution to its energy crisis. Nuclear energy is seen as one of solutions. But many parties in Indonesia refuse the nuclear alternative for several reasons, including the country’s geographic position and widespread corruption.

Meanwhile, the section on Emergency Cooperation under Article 3, should not only deal with natural disasters but also times of political and social conflict. It is critically important that the government, as well as international and non-governmental humanitarian agencies all have free access to conflict areas where there is a community need for humanitarian aid.

Human trafficking is also a serious area in which the Indonesian government faces considerable challenges. Cooperation on this issue is critically important to both countries as trafficking can create security threats beyond the boundaries of any nation.

There is a need to set up an independent body with members from the government, parliament, and civil society from both countries to monitor the implementation of this agreement according to the values of transparency and with respect for human rights and democracy.

Let us not repeat the dishonesty and debacle that occurred between these two neighbors over East Timor.

Usman Hamid is executive director of the Commission for Missing Persons and Victims of Violence (Kontras). Eko Waluyo is the Coordinator of Indonesian Solidarity, Sydney.