An international team of 18 experts, expanding on a 2009 report about "planetary boundaries" for safe human use, also sounded the alarm about clearance of forests and pollution from nitrogen and phosphorus in fertilisers.
"I don't think we've broken the planet but we are creating a much more difficult world," Sarah Cornell, one of the authors at the Stockholm Resilience Centre which led the project as a guide to human exploitation of the Earth, told Reuters.
"Four boundaries are assessed to have been crossed, placing humanity in a danger zone," a statement said of the study in the journal Science, pointing to climate change, species loss, land-use change and fertiliser pollution.
Of a total of nine boundaries assessed, freshwater use, ocean acidification and ozone depletion were judged to be within safe limits. Others, including levels of airborne pollution, were yet to be properly assessed.
The report defined climate change and loss of species as two core areas of concern. Each "has the potential on its own to drive the Earth System into a new state should they be substantially and persistently transgressed," the authors wrote.
Rising concentrations of carbon dioxide, the main greenhouse gas, are about 397 parts per million in the atmosphere, above 350 ppm that the study set as the boundary for safe use.
Almost 200 governments will meet in Paris in late 2015 to try to agree a deal to limit global warming to avert floods, droughts, heatwaves and rising sea levels blamed on rising emissions of greenhouse gases.
The study said that rates of extinctions of animals and plants, caused by factors ranging from pollution to deforestation, were 10 to 100 times higher than safe levels.
"Transgressing a boundary increases the risk that human activities could inadvertently drive the Earth System into a much less hospitable state," said lead author Will Steffen, of the Stockholm Resilience Centre and the Australian National University, Canberra.
The report expanded definitions of the planetary boundaries set in 2009, making it hard to compare trends.