The girls’ parents said they hoped the 31-year-old would spend the rest of his life in jail.
Kevin and Nicola Wells and Leslie and Sharon Chapman had hoped Mr Justice Moses would order Huntley should never be considered for release.
And, after the hearing at the High Court in London, the two families said: “We understand judges can only sentence on the facts of the case put before them.”
In a statement, they added: “We hope Ian Huntley spends the rest of his natural life in prison.”
Mr Justice Moses ruled that Huntley must serve a 40-year jail term before being considered for parole.
Holly and Jessica, both 10 and from Soham, vanished after leaving Holly’s home in August 2002. Their bodies were found in a ditch two weeks later.
Huntley, a caretaker at the secondary school in Soham, and his then girlfriend Maxine Carr, now 28, a teaching assistant in the girls’ class, told police they knew nothing of the circumstances surrounding the girls’ disappearance.
But it emerged at their trial at the Old Bailey in December 2003 that Huntley had met Holly and Jessica as they walked past his home, enticed them inside and killed them before hiding their remains.
Huntley was given two life terms for the girls’ murders - which Mr Justice Moses said would run concurrently.
The judge said in considering the minimum term Huntley should serve he took into account representations by Huntley’s lawyers and statements from Holly and Jessica’s families.
He said: “I have considered whether there are proven features of this case which (justify) a whole life order.
“But the case lacks a proven element of abduction; the meet between the girls and the defendant, whilst the other defendant Carr was away, was plainly by chance.”
He said he took into account “aggravating features” of Huntley’s crimes.
“In particular he must have killed one of the girls to avoid that girl disclosing his murder of the first.
“He must have killed her when she knew what he had done to her friend.”
Mr Justice Moses added: “The order I make offers little or no hope of the defendant’s eventual release.”