Rising carbon dioxide emissions are set to make the world's staple food crops less nutritious, according to new scientific research, worsening the serious ill health already suffered by billions of malnourished people.

The surprise consequence of fossil fuel burning is linked directly to the rise in CO2 levels which, unlike some of the predicted impacts of climate change, are undisputed. The field trials of wheat, rice, maize and soybeans showed that higher CO2 levels significantly reduced the levels of the essential nutrients iron and zinc, as well as cutting protein levels.

"We found rising levels of CO2 are affecting human nutrition by reducing levels of very important nutrients in very important food crops," said Prof Samuel Myers, an environmental health expert at Harvard University, Boston, and lead author of the study. "From a health viewpoint, iron and zinc are hugely important."

Myers said 2 billion people already suffer iron and zinc deficiencies around the world. This causes serious harm, in particular to developing babies and pregnant women, and currently causes the loss of 63m years of life annually. "Fundamentally the concern is that there is already an enormous public health problem and rising CO2 in the atmosphere will exacerbate that problem further."

While wheat, rice, maize and soybeans are relatively low in iron and zinc, in poorer societies where meat is rarely eaten they are a major source of the nutrients. About 2.4bn people currently get at least 60% of their zinc and iron from these staples and it is over 75% in Bangladesh, Iraq and Algeria.

"This is yet another example of the impact climate change is already having on people's ability to grow and access the nutritious food they need," said Hannah Stoddart, Oxfam's head of policy for food and climate. "With 25 million more children under five at risk of malnutrition by 2050 because of climate change, action to cut emissions and support communities to adapt is crucial."

The research, published in the journal Nature, represents a major advance in the understanding of how rising CO2 levels affect food nutrition. The scientists compared nutrient levels in field crops grown in ambient CO2 levels, about 380-390 parts per milliion (ppm) at the time of the work, with those grown in the elevated CO2 levels expected by 2050. The latter level, 545-585ppm, is expected even if substantial curbs on emissions are put in place by the world's governments. In order to take account of variable growing conditions, the researchers analysed 41 different strains grown in seven locations on three different continents.

Wheat grown in high CO2 levels had 9% less zinc and 5% less iron, as well as 6% less protein, while rice had 3% less iron, 5% less iron and 8% less protein. Maize saw similar falls while soybeans lost similar levels of zinc and iron but, being a legume not a grass, did not see lower protein.

The precise biological mechanism that causes nutrient levels to fall is not well understood as yet. But Professor Brian Thomas, a plant develoment expert at the University of Warwick and not involved in the research said: "The work is convincing and consistent with what we do know about the plant physiology."

The impact on human health resulting from the drop in the level of protein is less clear than for the zinc and iron loss. Myers said the resulting increase in carbohydrate in the crops could increase the rate of metabolic syndrome, the diabetes, heart disease and stroke that currently afflicts many in developed countries due to high levels of obesity. But Myers said obesity is not necessary for the risk of metabolic syndrome to rise. "It is something to do with the switch of foods itself."

Myers said simply eating more staple foods to meet zinc and iron requirements was not realistic when food production already must double by 2050 to meet the demand of rising populations. Some of the varieties used in the research performed better than others, raising the prospect of breeding strains that are less vulnerable to rising CO2. But the researchers noted: "Such breeding programmes will not be a panacea for many reasons including the affordability of improved seeds and the numerous criteria used by farmers in making planting decisions that include taste, tradition, marketability, growing requirements and yield."

Myers acknowledged that rising CO2 can improve crop yields on some circumstances, but said: "There may be a little positive effect, but the people who work in this area would not want to hang their hat on that in the face of the many other negative effects of climate change, including heatwaves droughts and floods."

April saw the first month for millions of years in which the CO2 level was greater than 400pm every day: before the industrial revolution started the large-scale burning of fossil fuels the level of CO2 in the atmosphere was 280ppm.

Myers told the Guardian: "It is very hard to predict all the challenges to human health resulting from climate change. My guess is there will be many more surprises as we remake the environmental conditions on the planet. As a civilisation we are now living with 400 ppm for the first time: it's a new world."