Canberra – Australia and Indonesia will strengthen their defence relationship on issues such as terrorism, regional security and piracy, Defence Minister Joel Fitzgibbon said Thursday.

Speaking after his first meeting with his Indonesian counterpart Juwono Sudarsono in Canberra, Fitzgibbon said the military chiefs of the two countries would work on practical measures of future cooperation.

The announcement comes just six weeks after a new security pact between the at times testy neighbours came into force.

Known as the Lombok Treaty, the agreement replaces an earlier pact torn up by Indonesia some eight years ago over Australian support for the independence of East Timor.

The new agreement includes a key Indonesian demand that Australia will not support separatist causes in its giant Muslim neighbour's sprawling archipelago.

"Australia and Indonesia have a confident and maturing defence relationship, based on a foundation of mutual respect and trust," Fitzgibbon said in a statement.

"We would like to deepen and expand (it) on matters affecting our common security interests such as terrorism, regional security and piracy." Military chiefs would develop joint understandings on mutual priorities for defence cooperation, he said.

These would include combined exercises and maritime surveillance and patrols as well as military training, postgraduate education, study visits and exchanges.

"We also explored mutually beneficial opportunities for defence industry cooperation and ways to support capacity building and management through, for example, joint science and technology projects," he said.

"The joint understandings will be guided by the Lombok Treaty and reflect the strengthening relationship between the two countries."

At the time the treaty came into force on February 7, Foreign Minister Stephen Smith said the countries also agreed to renew for three years a separate agreement on combating terrorism.

A total of 92 Australians were killed in bombings by militant Islamists on the Indonesian resort island of Bali in 2002 and 2005.

Smith said Indonesia was central to Australian foreign policy under the government of Prime Minister Kevin Rudd, which came to power in November elections.