The government was hoping to sign off on the final wording at the ASEAN conference in Singapore this week, but the Indonesian side may seek a commitment from Australia first.
Finance minister Mathias Cormann has conceded a long-anticipated trade deal with Indonesia may not be finalised before the end of the year as previously expected.
But Mr Cormann insists it will go ahead, despite Indonesia's anger over Australia considering moving its Israel embassy.
The government had expected to sign the document on the sidelines of the ASEAN summit in Singapore this week, but those plans are on hold.
“We are keen for that to happen by the end of the year but if not, then it will be soon thereafter,” Senator Cormann said on Wednesday.
In October, the prime minister said he was “open” to moving Australia’s embassy in Israel from Tel Aviv to the city of Jerusalem, and formally recognising the city as Israel’s capital.
The move would be deeply unpopular in Muslim-majority Indonesia, where analysts have warned Islamic groups would turn the matter into a domestic political ‘flashpoint’.
Embassy issue not raised
The move also prompted warnings from senior ministers in the Indonesian leadership, who said the move could jeopardise a peaceful solution to the Israel-Palestine conflict.
Senator Cormann spent five days in Indonesia last week, and insists no one from the Indonesian government ever raised the Israel matter.
“As I indicated last Friday, that has not been put to me,” he said.
Opposition leader Bill Shorten said he wished Scott Morrison well on his overseas trip, but said his “one foreign policy request” was that the government “stop this discussion” about moving the embassy.
“For goodness sakes, stop this discussion about moving the embassy from Tel Aviv to Jerusalem,” Mr Shorten said.
“Only Guatemala and the United States have proposed moving the embassy, it's an issue which has caused a lot of upset in the region.”
“If Mr Morrison doesn't intend to move the embassy he should just say so. Our lives are too short to be imitating a thought bubble.”
Mr Morrison arrives in Singapore Tuesday evening, kicking off a string of international summits.