In April, dozens of airlines received a letter from China's Civil Aviation Administration demanding airlines stop listing self-ruled Taiwan as a country.
Qantas had until mid-2018 to make changes, but announced on Monday it will follow Beijing's description of Taiwan.
"Our intention is to meet the requirements. It is just taking time to get there," CEO Alan Joyce told reporters at the annual meeting of the International Air Transport Association (IATA).
In a statement, Qantas executive team told Business Insider that the change will affect the entire Qantas Group and that there is "some complexity to work through."
"The IT and technology that underpins our websites and the connectivity takes time for us to get to grips with changes that need to be put into the programming stages of that," the statement read.
A spokesman for IATA recently told Business Insider that IATA and its member airlines have "no wish to make political statements" in their descriptions of markets. But in cases where there are no global standards, or "gaps" in how governments implement them, "we ask that they [governments] sort out their differences so that airlines are not caught in the middle."
"It is particularly tricky when government requirements are politically rather than operationally motivated," the spokesman said.
He added: "An inter-governmental agreement on the naming and grouping of states and territories would be a helpful reference. In the meantime, airlines wishing to serve the China market are doing their best to comply with China’s very stringent requirements."
Asked about whether Qantas' decision sets a worrying precedent, Australia's Foreign Minister Julie Bishop told Business Insider that "the decision of how Qantas structures its website is a matter for the company's management."
But she hinted at frustration about Beijing's moves.
"Private companies should be free to conduct their usual business operations free from political pressure of governments," Bishop said.
More than a dozen airlines, including Air Canada, Air France, and Malaysia Airlines, have changed their references to Taiwan since Beijing's letter was sent in April. Lufthansa and British Airways both made similar changes earlier this year, after Delta Air Lines was censured for listing Taiwan as a country on its website.
South Africa's national carrier SAA refers to its flights to Taiwan's capital as "Taipei, China" in its booking system.
After the Delta incident, Beijing reportedly called in representatives from 25 air carriers to demand they remove references to Taiwan as a country. China has since cracked down on a number of foreign companies, including Marriott, Gap, and Muji, for similar descriptions of Taiwan.
United Airlines and American Airlines, which received also the letter from China's CAA, have yet to make changes to their website or indicate any intention to do so.