Australia also showed significant improvements in overall five-year cancer survival, whereas New Zealand had a minimal increase.
Royal New Zealand College of General Practitioners president Dr Samantha Murton said it was "a significant concern" that New Zealanders were disadvantaged compared to their Australian counterparts.
"There are many causes and we need further research, but if we can make progress with health inequities, and cardiovascular and cancer treatment as suggested in the paper we might make some inroads and reduce the burden on patients and an already strained health system."
The research also found that Australia had an advantageous ageing structure compared to New Zealand, although in both countries indigenous populations were significantly disadvantaged when compared to the general population.
Aussies would also live longer and the life expectancy gap was expected to widen further by 2050.
In both countries, there was likely to be a spike in the number of people aged over 60 in the next 30 years, with people older than 80 increasing by 200 per cent.
The research also meant that public health policy needed to target ageing in New Zealand as a major goal in advancing the Ageing Well policy advocated by the Government.
"The ageing of our population is something that we are going to have to deal with in general practice," Murton said.