The ATO on Thursday applied for both of owner Nathan Tinkler's teams, the Knights and the A-League's Newcastle Jets and their parent company Hunter Sports Group, to be wound up due to unpaid debts.
According to documents filed in the Federal Court in Sydney, the Knights owe more than $1.4 million to the tax office, the Jets owe just over $1 million, while Hunter Sports Group is $184,000 in the red.
However NRL interim chief executive Shane Mattiske said he was confident the future of the Knights was not under threat.
"In relation to the ownership by Hunter Sports Group, guarantees have been put in place by the Commission to safeguard the Knights position," Mattiske told AAP.
"Those safeguards were a condition of ownership and are there to ensure the club's future."
A $20 million bank guarantee was a condition of Tinkler's privatisation of the club.
Hunter Sports Group said they had not been advised of the ATO's move to appoint a liquidator and that monies owed to the tax office would be paid.
"We are surprised by the move by the ATO, as we have not received notification of this move," Hunter Sports Group said in a statement.
"We advise that any outstanding sum will be paid as soon as possible - well before the reported hearing date on the matter next February."
Gold Coast Titans suffered a series of financial problems before being granted a new NRL licence by the ARL Commission in November after meeting a series of restrictions imposed upon it by the game's governing body.
But Mattiske said the future of the Knights remained on sure ground.