German news agency dpa reported that a Luftwaffe A310 medevac plane will fly ICU patients from the southern town of Memmingen to North Rhine-Westphalia state on Friday afternoon.
It is the first time the air force has used its so-called "flying intensive care units" - planes fitted with up to six ICU beds - to transfer Covid patients within Germany.
Hospitals in southern and eastern regions of Germany have warned they are running out of intensive care beds because of the large number of seriously ill patients.
The country’s disease control agency said 76,414 newly confirmed cases were reported in the past 24 hours.
Also on Friday, German Health Minister Jens Spahn said airlines coming from South Africa will only be able to carry German citizens, and travellers will need to go into quarantine for 14 days whether they are vaccinated or not.
"The last thing we need is to bring in a new variant that will cause even more problems," he said.
It comes after Angela Merkel backed calls for tighter restrictions amid surging Covid cases.
"It is of course a very sad day that we have to mourn 100,000 victims of the coronavirus," Merkel said at a news conference in Berlin on Thursday. "And unfortunately, at the moment, more than 300 deaths are being added to that each day."
The long-time German leader, who is currently in office as caretaker until her successor is sworn in, warned that hundreds more deaths were already looming.
"(The deaths) correlate very clearly with the number of infections that are occurring," she said. "We know how many people on average do not survive this disease."
"The situation is so serious because we are still in an exponential growth and because the cases that we see getting sick today are basically the patients who will be in intensive care in 10 or 14 days," Mrs Merkel said.
Reports in the Bild Newspaper claimed that Merkel wanted to impose a new lockdown on Germany, but was thwarted by the incoming government.