Ties between Australia and China, its largest trading partner, are at a low ebb after they clashed over a number of issues including trade, the origins of Covid-19 and accusations from Australia of Chinese political interference.
"From an Australian point of view, we understand the complexity of the relationship ... but China is seeking to shape the world around it in ways we have not seen before," Marles told ABC television.
"All of that I think is going to make it a pretty challenging pathway forward."
Anthony Albanese, who was sworn in as Australia's 31st prime minister on Monday, said the bilateral relationship would remain "a difficult one", before he left for a Quad summit in Tokyo with US President Joe Biden and the prime ministers of Japan and India.
The Quad is an informal security grouping seen in Beijing as an attempt to counter China's growing influence in the Indo-Pacific region.
A Xinhua report said Chinese Premier Li Keqiang on Monday sent a congratulatory message to Albanese over his election win, possibly ending a two-year Chinese diplomatic freeze of Australia.