Foreign minister Julie Bishop is convinced the letter from Tony Abbott to Indonesian President Susilo Bambang Yudhoyono will smooth the troubled waters between the two countries over the phone-tapping allegations.
The Indonesian president is still considering in detail the prime minister's response, sent over the weekend, and is expected to wait several days before responding.
In Perth for a leadership event, Ms Bishop says she's still on speaking terms with her Indonesian counterparts, and sees a fruitful future between the two countries.
"I am (confident) - the relationship is far too important for both countries, and we will work very hard to build on the relationship that already exists," Ms Bishop said.
"We must overcome these challenges and keep building on it. The prime minister has written back to President Yudhoyono ... and I hope that will assist in building the relationship."
Ms Bishop confirmed she had been in contact with her counterpart Marty Natalegawa since the revelations about the surveillance on the phones of the Indonesian president, his wife and Mr Natalegawa himself.
And she reiterated there would be no running commentary on intelligence matters in public.
"It is one of the most important relationships we have, and the Abbott government is determined to ensure whatever challenges we are currently facing in that relationship, we work very hard to establish bonds that will endure," Ms Bishop said.
Ms Bishop said a recent audit of the practical ties between the two countries revealed 22 Australian government departments and agencies were engaged in 60 major projects with Indonesian interests.
"Education, through to trade, agriculture, environment, scientific research collaboration, AFP, defence - you name it, across government we have very deep connections," Ms Bishop said.
"We work very hard to build the relationship, we recognise it's important - but other than that we are not going to comment on intelligence matters, and we cannot comment on intelligence matters.
"It would not be in our national interest, and it would not be in the interest of other countries."
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