The state's Health Minister, Brad Hazzard, said a “fairness issues” drove the government’s decision to U-turn for a short period.
The airline also announced seats will now be kept free between travelling groups, food and drink will not be served on board and lounges and valet parking will close.
Queensland Airports Chris Mills also said the decision to shut off the state from NSW and ACT led to an immediate reduction in flight schedules.
The announcement came as the business revealed a half-year loss of $54 million – with passenger numbers down 96.6 per cent in the second half of 2020.
On Monday, the PM told reporters it was “for others to judge” whether Premiers were doing the right thing but that they had to “explain the decisions”.
FlyPelican has extended its return flights between Canberra Airport and Byron Bay for a further eight weeks, due to strong demand.