The growth could ultimately lead to a 20-metre rise in sea levels and an increase of three degrees in temperature, the organisation said in its annual Greenhouse Gas Bulletin.
Atmospheric concentrations of carbon dioxide (CO2) have now reached 403.3 parts per million (ppm), up from 400.0ppm in 2015.
The two other main greenhouse gases, methane and nitrous oxide, also hit record concentrations last year.
Scientists say last year’s rise in CO2 was due to a combination of human activities, such as coal and oil emissions and deforestation.
The El Nino weather pattern also increased levels last year.
Concentrations are 45% above pre-industrial levels (since 1750), said the WMO.
They are also considerably outside the range of 180-280ppm seen during cycles of ice ages and warmer periods.
“Today’s CO2 concentration of 400ppm exceeds the natural variability seen over hundreds of thousands of years,” said the WMO.
The last time carbon dioxide levels reached comparable levels was three to five million years ago, in the mid-Pliocene era.
“During that period, global mean surface temperatures were 2-3C warmer than today,” said the WMO.
“Ice sheets in Greenland and West Antarctica melted and even parts of East Antarctica’s ice retreated, causing the sea level to rise 10-20 metres higher than that today.”
Scientists can discover pre-historic carbon dioxide levels from tiny air bubbles trapped in ancient Antarctic ice cores.
Even older data can be derived from fossils and chemicals trapped in sediment.
WMO chief Petteri Taalas said “there is hope” to reverse the concentration rates but insisted the time to act was now.
“Without rapid cuts in CO2 and other greenhouse gas emissions, we will be heading for dangerous temperature increases by the end of this century, well above the target set by the Paris climate change agreement,” he said in a statement.
The Paris agreement seeks to limit the rise in temperatures to “well below” 2C (3.6F) above pre-industrial times.
The news will add pressure to a meeting of environment ministers from around the world in Bonn next month to discuss implementing the Paris agreement.
It was dealt a blow last month when the US President Donald Trump said he planned to pull the United States out of the deal.
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