Indonesian Vice President Jusuf Kalla has said the relationship between Indonesia and Australia is "much better" as Justice Minister Michael Keenan became the first Australian minister to visit the country since the Bali nine executions.

Mr Keenan, the minister assisting the Prime Minister on counter terrorism, is in Jakarta this week to discuss Islamic State and foreign terrorist fighters with his Indonesian counterparts.

He said the relationship between the two countries was "very strong" and announced they would co-host the first counter-terrorism financing summit in the region in November.

Mr Kalla said there were some ups and downs in the relations due to the death penalty and other issues.

"Now I think it is getting normal compared to a few months ago.

"The Australian ambassador has come back ... Every month there is one Australian minister coming to Jakarta."

Trade Minister Andrew Robb is also planning a trade mission to Jakarta later this year after an earlier delegation was shelved in March due to tensions over the executions.

Mr Keenan's visit represents a further thaw between the countries after Foreign Minister Julie Bishop met her Indonesian counterpart Retno Marsudi at ASEAN and signalled the relationship was back on track.

He said the summit, to be held in Sydney in November, would boost efforts to track terrorism financing to counter the terror threat and combat transnational crime in the critical parts of the region.

Mr Keenan said that when Australia's terror alert was raised to high last year, the Coalition Government invested $20 million to stop cash being funnelled to terrorists from Australia, and to crackdown on transnational crimes that fund the drug trade such as crystal meth.

"This counter-terrorism financing summit reinforces the Coalition Government's priority to stop cash being funnelled to terrorists from Australia," Mr Keenan said.

He said both governments were very concerned about the reach of terrorist organisations in the Middle East and the methods used to radicalise people.

"We are very concerned about the radicalising of young Australians," he said.

There have been two terror attacks on Australian soil - the Martin Place siege and the 2014 Endeavour Hills stabbings.

Mr Keenan said there was a long history of cooperation between the two nations following the Bali bombings and it was good for him to see how the Indonesian government was dealing with the challenge of terrorism.

"The most important thing we can learn from Indonesia, which is the world's largest Muslim country, is the great tradition of tolerance and respect that Indonesians have for one another," Mr Keenan said.

"They are really a great example to the rest of the world about how to run a multi faith society.

"These are values we share in Australia today."