"It would be wrong of me to talk about what I've said to the president before the president has actually received it," he said.
"I just want to stress that as far as I am concerned, one of the fundamental tasks of any Australian government but certainly one of the fundamental tasks of my government is to ensure that our relationship with Indonesia goes from strength to strength," he added.
On Friday, more than 400 hard-line Muslims hurled bottles, tomatoes and eggs at the gate of the Australian Embassy in Jakarta to protest the alleged wiretapping.
They burned replicas of the U.S. and Australian flags while chanting for the Australia ambassador to be expelled, South Jakarta Police Chief Col. Wahyu Hadiningrat said. He said nearly 500 policemen were deployed to protect the embassy, which had been closed for two days by demonstrators.
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Associated Press writer Ali Kotarumalos in Jakarta, Indonesia, contributed to this report.