Barnaby Joyce has accused Malcolm Turnbull of throwing petrol on a fire by criticising a government proposal to move Australia's embassy in Israel.

Mr Turnbull warned shifting the embassy from Tel Aviv to Jerusalem would cause a negative reaction from Indonesia after meeting with its president Joko Widodo in Bali on Monday.

"Apparently we sent him over there because he's mates with Joko Widodo but my gosh if there was a small problem, he threw petrol on it," Mr Joyce told 2GB on Wednesday.

The former Nationals leader said the decision to send Mr Turnbull as Australia's representative hadn't worked.

Liberal MP Craig Kelly, who backed dumping Mr Turnbull as prime minister, said he had to decide whether his actions were helping or hindering the government.

"He doesn't speak for the government, he speaks for himself," Mr Kelly told Sky News.

"I think it's a very fine line that he's treading."

Prime Minister Scott Morrison says the government is still going through the process of looking at the embassy relocation, after floating the idea during the final week of the Wentworth by-election.