Mr Ball said CO2 had been demonised by "the greens" who "want society to collapse". He questioned whether there was enough CO2 in the atmosphere to have a damaging effect, whether the polar ice-caps were melting and whether the earth was heating up to a worrying extent.
After what was billed as a motivational lecture, a scientist based at the university called it "a rant in denial of climate change" and said Mr Ball "should not be allowed to explain to children what science is about again".
But Professor Mary Bownes, Edinburgh University's vice-principal, said she was happy with Mr Ball's Royal Society of Edinburgh Christmas lecture, saying it would stimulate debate.
The lecture started much as expected. Mr Ball came bounding on stage with enthusiasm and bad jokes. He used balls, string and snooker cues as props to explain how gravity was discovered not just by Newton, but by a "chain of people" including Galileo, Kepler, and Newton. In fact Newton, he explained, really just put together the work of Galileo and Kepler.
"He put two books together and called it gravity," said Mr Ball. "The greatest British scientist read two books. To be a genius, all you have to do is read the books. It might be two, it might be a dozen, it might be 30 or 40."
But after a song about John Dalton's atomic theory, the tone shifted and Mr Ball launched his attack on global warming. He said "the greens" had decided to "demonise" CO2 emissions and questioned whether CO2 could be poisonous, given that it makes up just one particle in every 3,000 in the atmosphere.
He said the earth had heated up by just 0.5 of a degree in the past 50 years and cast doubt over whether the polar ice-caps were melting, saying it depended on the time of year photographs were taken.
Mr Ball concluded by describing environmentalism as "worry science" and lamented the fact that in schools "seven out of 10 projects are about environmentalism".
At the end of the lecture Philip Wadler, a professor in informatics at Edinburgh University, accused Mr Ball of putting "fear, uncertainty and doubt" in the minds of young children, and challenged him to name one peer-reviewed article that supported his arguments. Mr Ball asked him to send him an email.
Reactions were mixed. Fiona Smith, an S3 pupil at St George's School in Edinburgh, said it was not what she had been taught but it was good to be "challenged".
But Professor Wadler's daughter Leora, 8, said: "The first part was good, but the second part was just him giving his opinion."