The question - which triggered a barrage of angry responses on social media - was asked by the Today programme presenter during an interview with physicist Brian Cox in the wake of Hawking’s death earlier today.
During the interview, which also included cosmologist Carlos Frenk, Humphrys asked: “One wonders a bit I suppose because you scientists, I’ve heard it said, can be a little bit competitive with each other, just occasionally.
“I wonder whether he was ever, or if it was ever said of him in your profession, that he was cut a bit of slack because he was so desperately disabled but fought through it?”
“No absolutely not,” Cox replied.
“He said himself, I think, that the realisation that he might not have long to live - as you said in your introduction - stimulated him to look more deeply into physics and give his life to physics, essentially.”
Humphrys’ query came after the 74-year-old broadcaster admitted that it was “probably the wrong question” to ask, following Frenk’s claims Hawking was forced to be more concise than other scientists because he was not able to write or type.
Hawking, a world-renowned physicist, was forced to rely on a wheelchair and a voice synthesiser after he was diagnosed with a rare form of motor neurone disease aged 22.
One listener wrote on Twitter: “The notion that disability affords a person some kind of bonus, ‘cut some slack’ by society that an able-bodied person would not receive, comes from a position of profound ignorance of reality.”
Another added: “How science seems to work in the brilliant mind of John Humphrys: Black holes don’t exist. We just let Stephen Hawking make them up because he couldn’t walk.”
Mark Atkinson, chief executive of disability charity Scope, said: “Stephen Hawking’s brilliance was an inspiration to countless people all over the world.
“His legacy shows just how important it is to not limit anyone because of their impairment or condition.
“If Stephen Hawking had been written off when he was diagnosed over half a century ago, he would not have continued his work and we’d all be worse off for it.”
The BBC declined to respond to Humphrys’ comments.