Talking to reporters, Turnbull denied allegations Australians had been refused entry to China, but admitted the the two countries had drifted apart following the introduction of the new legislation.
China is Australia's largest trade partner by a wide margin but the two countries have clashed in the past over political issues, including human rights and the alliance with the United States.
Turnbull added the relationship between China and Australia was very "deep and extensive," saying he regularly corresponded with Chinese president Xi Jinping.
Both Vanuatu and China have denied the reports, with Foreign Ministry spokesman Geng Shuang accusing Australia of "stirring up troubles" in his daily press briefing on Wednesday.
"The South Pacific Island countries should not be the sphere of influence of any country. Enough with certain Australian individuals' interference in other's internal affairs," he said.
New anti-influence laws planned
The proposed anti-influence legislation referenced by Turnbull has yet to pass into law, with some parts still in review by parliamentary committees.
Richard McGregor, senior fellow at Sydney's Lowy Institute, said the reforms were long overdue. "(This is) basic national security housekeeping," he said.
"There are some things Australia could have handled better, particularly the rhetoric surrounding this ... but if you're pushing back against China there's no nice way to do it."
Though Turnbull repeated the claim Wednesday that the laws weren't targeted at any one country, opponents have been quick to frame the legislation as "anti-Chinese."
"I would like to stress hereby again that we hope the Australian side will abandon the cold-war mentality and ideological bias, stop making irresponsible remarks and work with China," he told reporters.
The fight Australia had to have
A clash with Beijing over Australia's national security and political interference was a fight Canberra would have to have "sooner or later," Rory Medcalf, head of the National Security College at the Australian National University, told CNN.
"There are no good options here, if Australia was to ignore this issue it would get harder to push back in years to come and the kind of damage China could inflict would be greater," he said.
Medcalf said the dispute could in fact be the beginning of a more sustainable relationship between China and Australia if it was resolved properly. "The markers will be laid down about Australian independence and sovereignty," he said.
In recent years, the Australian government has found itself caught between its longstanding military alliance with the United States and its growing economic dependence on China.
Addressing this issue, Medcalf said the most important diplomatic task for Australia going forward was to "deepen and diversify" its security and diplomatic links with a range of countries.
"So no one country can inflict irreparable harm on Australia," he said.