Similar increases had been seen in both men and women, it said.
The child obesity rate has also increased from 8 per cent in 2006/07 to 10 per cent in 2011/12.
Excess weight was a leading contributor to a number of health conditions including type 2 diabetes, ischaemic heart disease, stroke and several types of cancer, the report said.
Obesity rates were higher among Pacific adults (62 per cent) and Maori adults (44 per cent), and Pacific children (23 per cent) and Maori children (17 per cent).
The report also stated obesity was strongly associated with socioeconomic deprivation, and child obesity rates were much higher among children living in the most deprived areas.
"New Zealand has high obesity rates compared with other OECD countries, although a similar obesity rate to Australia,'' the report stated.
"New Zealand's adult obesity rates, including those for European/Other adults were above the OECD average of 22 per cent."
If current trends continued, obesity would overtake tobacco use as the leading risk factor for disease by 2016, it said.
Green Party health spokesman Kevin Hague said the country couldn't afford the rising cost of obesity-related disease.
"Hitting the one million mark should be a huge wake up call to the Government.
"The Ministry of Health report also confirms another new high, with 225,700 people now having been diagnosed with diabetes and 25.5 percent of adults having `prediabetes' - that's a quarter of the population."
At the current rate, New Zealand would be hit with a "tidal wave of diabetes and heart disease", which would "cripple New Zealand's health system", Mr Hague said.
"The overtaking of the health system by diabetes and obesity will mean that the other health needs of New Zealanders will not be able to be met by our increasingly strained health system.
"The Minister of Health has committed $60 million a year to diabetes and obesity prevention, which is an almost 30 percent decrease in funding since 2008; all the while obesity and diabetes rates soar".
