Australians stranded in Peru, Argentina and South Africa amid the coronavirus crisis will be brought home on a series of Qantas flights over the next week, the Federal Government has announced.

Key points: Flights from the three destinations will depart in the coming weeks

Flights from the three destinations will depart in the coming weeks The Government is negotiating to organise further flights

The Government is negotiating to organise further flights Thousands of Australians are believed to be stranded overseas

Foreign Minister Marise Payne said 280 Australians had already left South America on a previously arranged flight.

She said an agreement had been struck between the Federal Government and Qantas to fly Australians stuck in the three countries home.

"The Australian Government is also assisting by ensuring that these flights have the necessary clearances and approvals in countries where Australian airlines normally don't fly," she said.

"Some of this is new for Qantas so we are assisting with that process."

Thousands of Australians remain overseas, and many have found themselves stuck in countries which have locked down their borders and imposed tough internal travel restrictions due to the pandemic.

The Federal Government has been negotiating access to those countries, after pleas for assistance from Australian citizens.

A flight left Santiago in Chile on Thursday morning after picking up Australians from Peru, at the cost of $2,550 per person.

Senator Payne said Australians would be expected to pay for a seat on the three confirmed Qantas flights, but emergency assistance would be available.

The Government is working to ensure Qantas is given the necessary clearances to fly. ( ABC News: Brendan Esposito )

"Australians are paying for those tickets themselves, where there is a great difficulty or a real difficulty for Australians to afford those flights, we have of course encouraged them to engage with friends, engage with family," she said.

"We also do have provision for traveller emergency loans."

Senator Payne said moves were underway to lock in further flights to Australia, including from India and the Philippines.

She said there were particular concerns for Australian citizens in India, which is in the middle of a country-wide lockdown.

"There are tens of thousands of Australians in India at any one time, many of them long-term residents of course," she said.

"We are actively trying to identify options for a commercial charter flight.

"The lockdown is continuing, and we will … provide advice to Australians as soon as we are able to."

Senator Payne said the Federal Government had worked with Qantas and Virgin to establish a network between the major transport hubs of Los Angeles, London, Hong Kong and Auckland across the next four weeks.