Tim Dodd – Indonesia's Foreign Ministry has a message for Australia that it evidently wants to be heard loud and clear, rather than in the confines of normally discreet diplomatic communication.

Yesterday, for the first time since 1999, senior officials from the two countries met in Jakarta for regional security and disarmament talks, which used to be held on a semi-regular basis until the East Timor crisis blew apart the relationship. In itself the meeting was a sign of further normalisation of Australian-Indonesian ties.

But in his opening statement to the meeting at Jakarta's Foreign Ministry, Indonesia's delegation leader, Makarim Wibisono, departed from his prepared statement to put on the record two issues that are bothering Indonesia regarding its southern neighbour.

One is alleged involvement by Australians in the independence movement in Indonesia's province of Papua, formerly known as Irian Jaya, which is the western half of the large island Australians know as Papua New Guinea. The other is the rocket-launching facility that Korean businessman David Kwan, with generous Australian government assistance, plans to build on Christmas Island, only 400 kilometres south of Indonesia's most populous island of Java.

Raising these two sensitive issues in yesterday's meeting, even though neither was listed on the agenda, would not in itself be unusual. What was interesting – and not expected by the Australian side – was that the Foreign Ministry raised the tempo by inviting journalists along to hear the opening statements, including Makarim's departure from his script.

It looks like a signal that despite the notable progress in relations since the low point after the Tampa affair and the asylum-seekers dispute a year ago, Australia should not take things for granted. This reminder from Indonesia hardly signals any major change in attitude.

Indeed the relationship is smooth at the moment and Makarim's tone yesterday was friendly. The two countries, as he mentioned in his opening statement, are co-operating in many areas. For example, in December, Australia and Indonesia will co-host an international conference in Bali on combating money laundering and terrorist financing, and in January they will jointly host a follow-up to this year's people-smuggling conference.

In his statement, after mentioning Papua and the Christmas Island launch pad, Makarim warned: "We must keep a vigilant eye on any issue that may come between us so that it will not grow into an irritant that can dilute the good relations and close co-operation [between us]."

Later during the morning coffee break, Makarim, who is director-general for Asia-Pacific and Africa, was more forthcoming on both issues. He acknowledged, with regard to Papua, that the Australian government did support Indonesia's territorial integrity. But he complained about Australian activists supporting the independence movement, an issue already being investigated by Indonesian diplomats in Canberra after an allegation by the Institute of Public Affairs in Melbourne that government money had supported Australian organisations involved in the Papuan independence struggle. "There are some people in Australia who are active in Papua and they agreed to clarify the matter," Makarim said.

The other issue, the Christmas Island launching pad, is less well known as a source of tension in Australian-Indonesian ties. But Korean businessman David Kwan has won whole-hearted endorsement from the Howard government for the project. The government agreed several years ago to spend $100 million on infrastructure – including a long runway to fly in the rockets – to help him realise his dream of a setting up a commercial rocket-launching venture on Christmas Island. (Conveniently for the government, the facilities are also supporting the new detention camp for asylum seekers on the island.) Using cheap Russian rockets, and with a position only 10 degrees south of the equator to take full advantage of the earth's rotation, Kwan believes he can break into this very competitive industry.

The problem, from Indonesia's point of view, is that his rockets will soar into orbit on a flight path that will cross 3,000km of eastern Indonesia. Legally this is not an issue because national airspace does not extend into outer space. But Indonesian parliamentarians have already voiced strong concern about the risk of accidents which could shower debris on Bali and Lombok.

Their concern is no doubt genuine, but people on the Australian side believe that Indonesia's real agenda is to try to establish the launch pad on Biak Island in Papua, which is positioned almost on the equator and already has a long runway. In reality, there is at present a glut of satellite-launching capacity and Kwan's venture faces an uphill struggle to get off the ground. But the issue has now entered bilateral security talks. Yesterday, during the coffee break, Makarim said there would be "a joint effort from both sides to eliminate adverse impacts, such as falling rockets".

Under Foreign Minister Hassan Wirajuda – a former diplomat appointed to the post just over a year ago – Indonesia's Foreign Ministry has gone the extra mile to improve relations with Australia, and was notably active in rebuilding ties in the aftermath of the Tampa affair when the Howard government was re-elected last year. Obstacles to the relationship are not likely to come from this source. Which means their message has to be listened to.