The CoC was signed by Natalegawa and Australian Foreign Affairs Minister, Julie Bishop, and was witnessed by Indonesian President, Susilo Bambang Yudhoyono, in Nusa Dua, Bali, on Thursday.
"Whether it will be complied with or not, only time will tell. However, this will be some sort of deterrent for the next Australian Governments that they will not do any tapping activity in the future," Natalegawa said during a press conference after the signing.
The signing of the Code of Conduct was within the framework of the security cooperation between the two countries called the Lombok Treaty, Natalegawa said.
It has two key constituent elements.
"First, the commitment on an agreement between the two sides not to use any of their intelligence including surveillance capacity and or other resources in way that could harm the interests of the parties," Natalegawa said.
The CoC will also make it possible for the two sides to enhance their intelligence cooperation.
"With the signing of the Code of Conduct, there will be a full restoration of communication between the armed forces of the two countries as they will be able to ensure the kind of cooperation that is needed in the future," the Minister said.
The basic message, is that with the signing of the CoC, both countries "are back to where we have been" and that will be also enhanced in the future, Natalegawa said.
"The most important thing is that we should be grateful after all of our efforts, they (Australia) are finally willing to sign (the CoC)," he said.
The CoC will be the basis to enhance intelligence cooperation between the agencies of the two countries, Julie Bishop said.
"And we both believe that the strong intelligence partnership is vital for both countries and is the most effective way to defeat those who could do harm to the people of Australia and the people of Indonesia," Bishop said.
The joint understanding will be a guide for regular contact between the respective heads of the intelligence agencies and institutions, and will promote dialogue and mutual understanding to work together to meet the challenges and respond to security threats including the threat of home grown extremists returning from conflict in the Middle East, Syria and Iraq, Bishop said.