Thousands of Australians defied federal government warnings not to travel overseas as the deadly coronavirus outbreak worsened – leading to many now being stuck abroad or on emergency flights home.

Prime Minister Scott Morrison said he was bewildered and frustrated by many of the 16,000 Australians who decided to head overseas despite the highest level of government advice not to.

“How they actually think they’re going to get back now is going to be very difficult,” he told Sydney radio 2GB on Friday.

“I don’t think they’ll find themselves high on the list.”

With the coronavirus pandemic sweeping the globe, the Department of Foreign Affairs and Trade issued “do not travel” advice for every country in the world on March 18.

It also urged all Australians overseas to head home as soon as possible, warning the country’s borders were likely to close altogether.

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Even earlier, on March 10, DFAT had told Australians – particularly those with underlying health conditions – to reconsider cruise travel because of the coronavirus spread.

Mr Morrison said travellers should have heeded the early advice.

“If people behave like that, then we lose lives,” he said.

“Honestly, I think it was still an indication that people just weren’t getting it.”

Mr Morrison said there were some exceptions among the 16,000 for people who had travelled for aid and scientific work.

Following the March 18 warning, the federal government closed Australia’s borders entirely on March 25. Days later, it required all returning travellers to spend their first 14 days back in Australia in enforced quarantine at hotels and other accommodation.

There are now thousands of Australians in hotels across the country, monitored by police and Australian Defence Force personnel.

Some have complained of the conditions, comparing them to prisons,

Others, however, say they understand the arrangements are necessary.

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There are also hundreds of Australians stranded in countries such as Peru, under military-enforced lockdowns and curfews.

A $5000-a-seat charter flight brought hundreds of Australians back from Peru earlier this week. Dozens were left behind because they could not get to the airport in Lima or had not bought tickets.

Tweet from @Smartraveller

Another flight brought Australian citizens and residents back from Nepal to Brisbane on Thursday.

Still more are stuck on cruise ships in Europe, the US and India. More than 130 are expected to fly home from Florida this weekend after two cruise ships carrying sick passengers were finally allowed to dock.

-with AAP