Health Minister Norman Lamb insisted no NHS cash has currently been allocated for payouts to victims who were sexually abused by the former Top Of The Pops host.
Mr Lamb added: "The claims handling co-ordination scheme... will, in the first instance, draw on the estate of Jimmy Savile to make payments to victims of abuse. If, in the future, the estate funds are exhausted, it is only then that claims may be funded from the public purse.
"The scheme covers claims which may arise in a variety of circumstances and is not restricted to alleged assaults on NHS premises."
A compensation scheme for Savile's alleged victims was approved following a ruling at the High Court in February, with the BBC saying payments will be capped at £60,000.
Mr Justice Sales put the current value of Savile's estate at £3.3 million after lawyers initially suggested it was around £4 million.
Some 140 people have come forward to say they were a victim of the DJ, who died in October 2011 aged 84.
Savile is thought to have used his position to abuse vulnerable patients, many of them children, at hospitals.
His links with 33 health institutions, including hospitals and a recovery home for children, are subject to an NHS investigation.
The final reports are expected to be completed by June, according to the Government.