The special flight is expected to take 15 hours and 35 minutes, a spokeswoman said, according to Deutsche press agency (dpa).
On board the flight to the Mount Pleasant military base are researchers from Germany's Alfred Wegener Institute and the new crew for a German research icebreaker, the Polarstern.
Once at the Falkland Islands, the crew will board the icebreaker and spend two months in the Antarctic's Weddell Sea collecting long-term data for climate forecasts.
In normal times the crew would fly over Argentina or South Africa on their way to the Antarctic. However, due to the pandemic, scheduled flights are out of the question.
Before departing on Sunday night, the passengers and Lufthansa crew had spent two weeks in quarantine.
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