Qantas says that proposed law changes limiting the airline's ability to hire foreign flight crews will force it to end services to Darwin and Cairns.
Chief executive Alan Joyce told a Senate inquiry in Canberra on Monday that the proposed bills would constitute a major threat to the airline's business, to Australian jobs, investment and growth.
He also warned that Qantas could be forced to sell its budget airline Jetstar if the federal government goes ahead with plans to tighten the Qantas Sale Act.
The BBC reports one bill would force Qantas to keep its main operations in Australia. Another bill seeks to amend aircraft crew laws.
The amendment to the Qantas Sale Act of 1992 requires that the majority of heavy aircraft maintenance, plus flight operations and training, be conducted in Australia.
Another proposed bill would require Australian airlines and their subsidiaries to offer the same wages and benefits to crew based overseas as to their local counterparts.
Mr Joyce says he has grave fears for the future of the company if the legislation goes ahead.