Australian Prime Minister Tony Abbott has told President Bambang Susilo Yudhoyono of Indonesiathat Australia will not take any action in future that will hurt relations between them.
There has been an outcry in Jakarta because of accusations that Australian agents tapped the phones of the president and his inner circle, and his wife, in 2009.
The president said Mr Abbott made the pledge in a letter to him hand-delivered to him on Saturday in Bali by former Army chief Peter Leahy - a move described by the government as a sign of respect,.
Mr Yudhoyono said the two countries would work on a new code of ethics for intelligence-sharing and described their relations as essentially very good, saying they needed to be safeguarded.
But he said bilateral cooperation would not resume until the Australian government signs new intelligence protocols and a code of ethics.
A presidential spokesman earlier said the letter was "in accordance to our expectations".
The ABC reports the president's comments were likely to be welcomed by the Abbott government, which was under increasing criticism over its handling of the situation.
Indonesia is a major importer of Australian wheat, live cattle and beef, while Australia is Indonesia's 10th largest export market.