Counsel for Gary Haggarty, 43, claimed proper access to a huge body of papers would show he has no case to answer on some of the allegations against him.
A prosecutor also indicated it was unclear when Mr Haggarty's trial will take place.
The allegations span a 16-year period.
It relates to the period from 1991 to 2007.
In January 2010, Mr Haggarty agreed to become an assisting offender under the terms of the Serious Organised Crime and Police Act.
Preliminary enquiry proceedings to establish if he will stand trial have been repeatedly put on hold as his legal team battles to gain access to unredacted interview material.
At one stage he also failed in a High Court bid to force the PSNI to hand over the tapes.
One potential solution involves prosecutors going through all the papers and using a system of ciphers for blanked-out names and passages.
At Belfast Magistrates' Court on Wednesday, defence counsel confirmed the charges are based on her client's admissions at interview.
Asked by the district judge why she needed full disclosure for a preliminary enquiry, the lawyer replied: "It's our clear view in respect of certain of these charges, were the papers disclosed in the appropriate form, it would show in certain charges there isn't a case to answer."
Pressed on this point, she added: "He has given an indication of matters he was involved in at the behest of, by licence of, and as an agent of the state.
"That's the position and that's why it's important."
According to a senior prosecuting lawyer there is no duty to disclose absolutely everything.
He suggested, however, that if the defence identified any charges in dispute, consideration would be given to making further disclosures.
With the cipher system to be completed in six weeks time, the judge listed the case for a further review at that stage.
Meanwhile, the judge resisted renewed calls to press ahead with preliminary enquiries for two Belfast men charged with murdering two Catholic workmen.
James Smyth, 48, and Mark Campbell, 43, are jointly accused of the double killing of Gary Convie and Eamon Fox in May 1994.
The victims were gunned down as they sat eating lunch in a car at a building site on Belfast's North Queen Street.
Mr Smyth, from Forthriver Link, and Mr Campbell, of Canning Place, are further charged with attempting to murder a third man, Donal Laverty, in the same attack.
They were charged by detectives investigating a campaign of UVF-linked murder and serious crime.
At previous hearings, defence lawyers claimed the allegations are based on evidence from Mr Haggarty.
In court on Wednesday, Mr Smyth and Mr Campbell's solicitor argued that their committal proceedings should be listed for eight weeks time.
With the prosecution stressing that timeframe will not be met, the judge asked whether their cases would have to wait until after Mr Haggarty is dealt with.
The prosecutor replied: "It's unclear whether there will be a Haggarty trial, but it will have to wait certainly until pleas have been entered and it's considered there's nothing more on the books."
He added: "Until we know the assisting offender's status as a witness we can't take a decision."
A loyalist supergrass charged with 212 offences, including five murders, may seek to have some charges dropped on the basis of having acted as a state agent, a court has heard.