"We will probably be able to continue the trip to Australia later this evening," delegation sources said in Abu Dhabi on Monday afternoon local time.
It is currently being examined whether the trip can be continued with the air force's aircraft or whether the delegation can take a scheduled flight.
Baerbock was due to arrive in Australia on Monday to kick off a week-long trip to the Pacific region which would also see her hold talks in New Zealand and Fiji.
However, after a stopover to refuel in Abu Dhabi, the flight carrying the German minister and her delegation had to dump fuel and turn around in the early hours of Monday.
A German Foreign Office spokesman who was on board explained that "due to a mechanical problem, we have to return to Abu Dhabi for safety reasons. Options for further travel arrangements are currently being clarified."
Shortly after take-off the captain informed passengers that there were problems with the retraction of the landing flaps.
The plane landed back in Abu Dhabi at 5.33am local time (1133 AEST).
There was no comment on what effect the delay may have on Baerbock's official engagements in Australia.
During her inaugural visit to Australia, Baerbock plans to visit Canberra and will meet with Foreign Minister Penny Wong in Sydney.
According to the German Foreign Office's website, the main topics Baerbock intends to discuss with partners in the region will be economic security, Russia's war against Ukraine and China's role in the Indo-Pacific.
Baerbock's agenda includes a visit to Australian agencies in the areas of cyber-security, disaster prevention and satellite manufacturing. The German minister will also visit a naval base of the Australian Navy.
On Tuesday in Canberra, Baerbock plans to take part in a ceremony for the return of cultural objects to representatives of the Indigenous Kaurna people at an institute for Aboriginal studies.
This is not the first time Germany's foreign minister has run into problems with a German government jet. In mid-May Baerbock was stranded in Qatar due to a flat tyre on her government jet in Doha.
Other members of the government have also had to make unscheduled stops due to issues with aircraft belonging to the German Armed Forces Air Service.
In November 2018 an air force Airbus carrying then chancellor Angela Merkel and her finance minister Olaf Scholz en route to the G20 summit in Buenos Aires had to turn back.
In October 2018, rodents chewed important cables on Scholz's aircraft during a stop in Indonesia. Scholz was returning from an International Monetary Fund meeting at the time.
The German government is "very satisfied" about the condition of the fleet of aircrafts, said deputy government spokesman Wolfgang Buchner in Berlin on Monday.
The army's air force "is doing an excellent job," Buchner said, adding that the aircraft are "excellently maintained".
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