The Pakistani heart and lung surgeon, who the late Princess of Wales described as "Mr Wonderful", is believed to have had a discreet two-year relationship with the royal that reportedly ended just months before her tragic death in a car crash in Paris in August 1997.
Dr Khan is pursuing Rupert Murdoch owned News International for substantial damages after Scotland Yard had informed him last year that it was possible his voicemails were hacked back in 2007.
But sources close to the 53-year-old told The Sunday Telegraph that he now fears the hacking may have begun a decade earlier.
"It is only when Dr Khan started to think back to the time when he was with Diana that it began to occur to him that someone may have been trying to listen in to his messages.
Their friendship was very private and very discreet but he now fears journalists were targeting him in a bid to find out what was going on.
He is very angry about it and it just shows how long ago this activity stretches back," the source was quoted as saying.
Dr Khan, from Jhelum in Pakistan, is pursuing the maximum compensation from News International and plans to donate the sum to a heart clinic for poor children he has set up near his hometown.
When he first learned that he may have been a victim of hacking, he had said: "To know that someone has been listening to your private messages is awful. It's absolutely terrible.
"It feels as if you have been robbed. I feel really violated. I am very angry."
Dr Khan met Princess Diana in 1995 when she was visiting the Royal Brompton Hospital in London where a friend was recovering from heart surgery.
They got close soon after but he later moved to Malaysia before returning to Pakistan.
Dr Khan had sent a statement to Princess Diana's inquest back in 2008 which confirmed their brief relationship.
His fears over the extent of media intrusion into the affair come at a time when Metropolitan police is believed to be investigating 600 fresh claims against Murdoch's News International.
Operation Weeting, the Met police's probe into the phone hacking scandal involving the now defunct News of the World tabloid, has led to nearly 250 legal claims against the company already.