The News of the World's covert surveillance of Prince William was allegedly commissioned while the paper was under police scrutiny for hacking into voicemail messages of members of the royal household.
Derek Webb, the private investigator who told Tuesday's Newsnight that he was paid by the News of the World to follow more than 100 targets over eight years until the paper was closed in July, said he was asked to follow Prince William in 2006 in Gloucestershire.
During the same year a Metropolitan police investigation into the hacking of the voicemails of members of the royal household led to the arrest of News of the World royal editor Clive Goodman and Glenn Mulcaire, a private investigator employed by the paper.
The police were called in after two diary items were published about Prince William in the News of the World's Blackadder column, which the royal household suspected could only have come from hacked voicemail messages.
Goodman and Mulcaire pleaded guilty to intercepting voicemail messages and were jailed in January 2007.
A spokesman for Prince William said: "Our position has been as it always has been, since 2006, and that is not to comment."
Among the 100 or more people Webb told Newsnight he targeted on the News of the World's orders were the former Labour home secretary Charles Clarke, John Prescott, Prince Harry's ex-girlfriend Chelsy Davy, London mayor Boris Johnson, and model Elle MacPherson.
Maxine Carr, the ex-girlfriend of murderer Ian Huntley, the Duke of Westminster, Sir Alex Ferguson and Sienna Miller were also on Webb's list.
Webb said the paper also paid him to conduct covert surveillance on Angelina Jolie, Simon Cowell, Sir Paul McCartney, David Miliband and Heather Mills.
Others he said he had followed for the paper included Gary Lineker, former attorney general Lord Goldsmith and Harry Potter actor Daniel Radcliffe's parents.
It was also reported on Tuesday that Webb tailed Tom Watson, the MP who helped expose the phone-hacking scandal in parliament, for five days during the Labour party conference in 2009.
Watson sits on the select committee that will grill News International chief James Murdoch for a second time on Thursday.
Webb, a former police officer who worked for many years in covert surveillance and received additional training from MI5, said there was nothing illegal in what he was doing and the paper was pleased with his work and kept commissioning him.
However, he said he felt NoW should have given him "loyalty money" for his eight years of service when it closed, but it refused.
News International declined to comment on Webb's claims. However, the News of the World's former features editor, Jules Stenson, appeared on Newsnight to defend the paper.
Stenson told Newsnight that Webb had been commissioned by the newsdesk, but the features desk had also used private detectives to pursue "the great and the good" for important scoops such as the revelation that Prince Harry had smoked cannabis.
He said it was common among the media to use private investigators and there was nothing wrong with it. "All media employ private eyes, that includes the BBC," he added.
"Investigative journalism is messy. The first goal of investigative journalists is to find the people. The crooks and villains aren't on the electoral roll, they're not on Acacia Avenue," said Stenson.
He told Newsnight that Webb's story was "one-sided" and "very slanted" and was the view of a man who had "a grievance" against the paper because he had been cut loose when it closed in July and he had not received compensation for loss of work.
Stenson's appearance on Newsnight was almost as significant as Webb's, as few top journalists have come out to defend the paper.
He said he was "extremely surprised" by revelations in the Guardian this week that his former paper hired Webb to run covert surveillance on two of the lawyers representing phone-hacking victims as part of an operation to put pressure on them to stop their work. Webb secretly videoed Mark Lewis and Charlotte Harris as well as family members and associates.