Professor Lynn, who has provoked controversy in the past with research linking intelligence to race and sex, said university academics were less likely to believe in God than almost anyone else.
A survey of Royal Society fellows found that only 3.3 per cent believed in God - at a time when 68.5 per cent of the general UK population described themselves as believers.
A separate poll in the 90s found only seven per cent of members of the American National Academy of Sciences believed in God.
Professor Lynn said most primary school children believed in God, but as they entered adolescence - and their intelligence increased - many started to have doubts.
He told Times Higher Education magazine: "Why should fewer academics believe in God than the general population? I believe it is simply a matter of the IQ. Academics have higher IQs than the general population. Several Gallup poll studies of the general population have shown that those with higher IQs tend not to believe in God."
He said religious belief had declined across 137 developed nations in the 20th century at the same time as people became more intelligent.
But Professor Gordon Lynch, director of the Centre for Religion and Contemporary Society at Birkbeck College, London, said it failed to take account of a complex range of social, economic and historical factors.
"Linking religious belief and intelligence in this way could reflect a dangerous trend, developing a simplistic characterisation of religion as primitive, which - while we are trying to deal with very complex issues of religious and cultural pluralism - is perhaps not the most helpful response," he said.
Dr Alistair McFadyen, senior lecturer in Christian theology at Leeds University, said the conclusion had "a slight tinge of Western cultural imperialism as well as an anti-religious sentiment".
Dr David Hardman, principal lecturer in learning development at London Metropolitan University, said: "It is very difficult to conduct true experiments that would explicate a causal relationship between IQ and religious belief. Nonetheless, there is evidence from other domains that higher levels of intelligence are associated with a greater ability - or perhaps willingness - to question and overturn strongly felt institutions."
