Coptic Pope Tawadros II was reluctant to say what he thought the Australian government should do with around 20 Coptic families currently facing deportation.
"The decision (is) up to the Australian authorities," he said.
"We appreciate generally any support for any Egyptian people," he added.
On Wednesday, the Pope met with the Prime Minister and Foreign Minister in Canberra but did not detail what those talks have covered.
He said the Australian government should assist his homeland.
"I ask the government here to support the education and the economy of Egypt," Pope Tawadros said.
"This is very important for the stability of the world."
Australia's Assistant Immigration Minister, Alex Hawke told SBS World News last week that no asylum seekers will be returned to Egypt while a state of emergency is in place.
"At the moment we're working through all of the cases," Mr Hawke said.
"We're applying a mix of permanent and temporary solutions, depending on people's individual circumstances," he said.
Coptic Christians are a persecuted minority in Egypt and are frequent targets for IS .
