Tim Hawking, 36, made the confession in an upcoming BBC documentary, while admitting that it was was only after his father got his synthesised voice that they were able to communicate properly.
Tim, who works for toy company Lego, said that he had never known his father as a healthy man.
The 73-year-old physicist was diagnosed with motor neurone disease in 1963.
Since 1985, Hawking has used a computer speech system to speak in a distinctive electronic voice.
"My dad was able to speak with his own, natural voice for those first years, but it was incredibly difficult to understand what he was saying - particularly for me at such a young age. As a three-year-old, I had no understanding of what he was saying," Tim was quoted as saying by 'metro.Co.Uk'.
"I didn't really have any communication with him for the first five years of my life. It was only when he got his voice synthesiser that I was actually able to start having conversations with him.
Tim is the third of Hawking's children with his first wife, Jane Wilde. Their romance forms the basis of the book and film 'The Theory of Everything'.
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