Mr Erdogan, who is under two weeks away from a federal election, made the comments at an election rally in northern Turkey.
“You heinously killed 50 of our siblings. You will pay for this,” Mr Erdogan said at the rally, in which he also aired segments of a livestream shared to Facebook by the Christchurch gunman.
Mr Erdogan also called on New Zealand to hand the Christchurch shooter the death penalty, and said that any anti-Muslim attacks in his own country would result in the offenders going home “in caskets”.
“Your grandparents came here… and they returned in caskets,” Mr Erdogan said, referencing the thousands of Australian and New Zealand soldiers who died during the Gallipoli Campaign in Turkey during World War I.
“Have no doubt we will send you back like your grandfathers.”
Mr Morrison said he did not accept that the President’s comments reflect the feeling of the people of Turkey and “all options were on the table” in terms of Australia’s response.
Mr Morrison met with the Turkish ambassador Korhan Karakoc at Parliament House on Wednesday morning.
“I do not accept the excuses that have been offered for those comments,” he said.
Opposition Leader Bill Shorten said Mr Erdogan’s remarks were “foolish and offensive”.
“Intemperate and regrettable remarks like this only play into the hands of those who seek to divide. They do not protect the peace and security of any nation,” he said.
Mr Erdogan is touring the country ahead of Turkey’s March 31 election.
Mr Erdogan has been president of Turkey since 2014, and was prime minister for the 11 years prior.