Huntley, who is serving a life sentence for killing schoolgirls Holly Wells and Jessica Chapman, had his throat slashed in March and now claims the prison service failed in their duty of care towards him.
A Ministry of Justice spokesman said: "Ian Huntley is bringing a claim against the Ministry of Justice following an assault by another prisoner.
"The claim is currently being vigorously defended."
The former school caretaker, who murdered the 10-year-old friends in Cambridgeshire in 2002, was left scarred by the attack at Frankland Prison, Co Durham.
He is alleged to have been attacked with a razor blade by Damien Fowkes and needed hospital treatment.
Earlier this year, then justice secretary Jack Straw said the government had "absolutely no intention" of paying compensation to Huntley over the attack.
The comments, at Commons question time, came as it emerged that Huntley could be awarded up to £20,000 in compensation if he sued for negligence.
It was reported last night that Huntley could claim nearly £100,000 in damages in a case that could cost tax payers more than £1 million in legal aid fees.
He is said to be seeking £20,000 for injuries and £60,000 for authorities failing in their duty of care, the Daily Mail said.
The newspaper also said he is expected to claim a further £15,000 through the Criminal Injuries Compensation Authority.
No paperwork in relation to the matter is believed to have been received by the body, however.
Speaking in March, Mr Straw said he agreed with the Conservative MP for Bracknell Andrew Mackay that if the murderer made a successful claim, it would be a case of "the compensation culture gone absolutely mad".
The attack on 36-year-old Huntley came on March 21. It was not the first time Huntley was attacked in prison.
An inmate threw boiling water on him while he was in the health care wing of high security Wakefield Prison, West Yorkshire, in September 2005. He also tried to commit suicide in prison on three occasions.
He was moved to HMP Frankland, a Category A high security men's prison, in 2008. That year, HM Inspectorate of Prisons raised concerns about violence at the jail.
Huntley was convicted in December 2003 of murdering Holly and Jessica after they vanished from their homes.
Along with his then girlfriend Maxine Carr, a teaching assistant at the girls' school, he initially told police they knew nothing of their disappearance.
But at his Old Bailey trial, it emerged Huntley met the girls as they walked past his home, enticed them inside, killed them and hid their remains. Carr was jailed for perverting the course of justice but has since been released.
If Huntley is successful in his bid for compensation, comparisons would no doubt be made with the amount of money awarded to Holly and Jessica's parents in damages for their murder at his hands.
The families each received £11,000 from the Criminal Injuries Compensation Authority. Figures paid out for the death of a child are lower than for the death of an adult because the financial impact is deemed to not be as great.
Juliet Lyon, of the Prison Reform Trust, told BBC Radio 4's Today programme: "The duty of care that prison staff have is a difficult one, but it is to hold people safely and securely, regardless of what they have done.
"The issue of compensation is a much more complicated one, but the issue of safety and security is a bedrock one... If a court sentences someone to custody, they are not sentencing them to be attacked.
"We have to expect that our prisons are going to be safe, secure places.
"If that breaks down, if the staff aren't able to hold that line, it is then up to the individual to pursue any means they are able to."
Ms Lyon said that notorious inmates often had to be kept separate from other prisoners for their own safety.
"With very high-profile cases, quite often people are held separately," she said. "They require a lot of extra supervision, with high numbers of staff if there is any locking or unlocking to be done.
"Undoubtedly, it's a very difficult thing to manage for staff working in an overcrowded system who get eight weeks' basic training. It's a very tall order.
"We have to look to ministers to be absolutely clear with the staff that they expect nothing less than a safe, secure system."
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