The prince and more than 40 others are suing News Group Newspapers (NGN) over accusations of unlawful activities by journalists and private investigators, for the Sun and the now-defunct News of the World from the mid-1990s to the mid-2010s.
The cases against NGN are due to go to a trial beginning in January.
In March, Harry, 39, sought to amend his lawsuit to add new allegations, including that the Sun ordered private investigators to target his then girlfriend - and now wife Meghan - in 2016.
However, in a ruling on Tuesday, Judge Timothy Fancourt refused him permission to extend the time frame of his claim to do so, and likewise rejected an application to include allegations dating to 1994 and 1995 involving his late mother, Princess Diana.
The judge also rejected an application from Harry and the claimants to include allegations Murdoch, 93, gave "knowingly false" evidence about his knowledge of phone-hacking and other unlawful acts, and was personally involved in a cover-up.
However, Harry was allowed to alter his case to include allegations the papers had bugged his landline phones, and the judge ruled the claimants could include accusations against more journalists and private investigators, and amend their case to bring more details of alleged lies by NGN to a public inquiry.
Fancourt told the court both sides had won about half of the disputed amendments, although NGN had won on more "big ticket" items such as bringing "Mr Murdoch personally into the matter".
In his written ruling, Fancourt said those pursuing the lawsuits against NGN could not resist adding more and more details, which he said were of great interest to "journalists who are looking for a good storyline to publish" but did not add any weight to the evidence.
"I also consider that there is a desire on the part of those running the litigation on the claimants' side to shoot at 'trophy' targets, whether those are political issues or high-profile individuals," he said.
"This cannot become an end in itself."
A spokesperson for NGN said the court had "thoroughly vindicated NGN's position", while the claimants said in a joint statement they were pleased the judge allowed them to amend their case on "a number of significant issues" such as allegations about deliberate destruction of evidence.
