But Mr Jones, 48, who has been on leave from his pounds 66,000-a-year post as Assistant Commissioner of the Metropolitan Police since the inquiry began, is contesting the process in the courts. His lawyers, Kingsley Napley, have lodged an application for judicial review.
Sources have confirmed that, although the decision has been made by Michael Howard, the Home Secretary, a formal application to the Queen for Mr Jones's Royal Warrant to be withdrawn will only be made if Mr Jones loses his legal challenge. If he succeeds, a financial deal involving compensation and a pension, such as that which ended the Alison Halford affair, appears likely.
Mr Jones, a high-flyer who had been in charge of personnel and training, is one of the six most senior officers at Scotland Yard who are appointed by Royal Warrant.
He went on 'gardening leave' following allegations that he had been involved with Asil Nadir. However, the inquiry, by Peter Nobes, then Chief Constable of West Yorkshire, cleared Mr Jones of any contact with the disgraced former head of the Polly Peck empire and concentrated on his lifestyle and conduct as a senior officer. It focused on allegations concerning use of police cars and the police river launch, and acceptance of hospitality on foreign trips.
The Crown Prosecution Service decided there was not enough evidence to bring criminal charges, but Scotland Yard pursued a series of disciplinary accusations which were heard at a tribunal last summer, where all sides were legally represented and which is believed to have found the majority of claims proved. The report was passed to the Home Office last year. Since no disciplinary processes existed for officers of Mr Jones's status, the mechanism had to be drawn up, based on existing procedures for senior ranking officers.
The legal battle could extend the process by another year and may lead to damaging revelations in public, as occurred in the Halford case.
Senior Scotland Yard officers are concerned that Mr Jones, who is said to maintain that he has been treated unfairly, will use the opportunity to disclose deep splits among the high command of the Yard. There are suggestions that Mr Jones's combative style did not find favour with some of his more conservative colleagues.
Mr Jones is said to have challenged the basis of the investigation, suggesting that it only arose through a lack of guidelines surrounding the conduct of senior officers in such areas as the acceptance of hospitality. Some of the allegations have been described as petty.
Mr Jones was in command of the police operation at Wapping in east London during clashes between police and pickets outside the News International plant in January 1987. The operation was later criticised after an inquiry by Northamptonshire Police.
A Home Office spokesman said last night: 'Michael Howard, the Home Secretary, has reached a decision on the case and in due course a report will be submitted to Her Majesty for consideration.'
Home Office sources also said the inquiry had cost far less than the speculated figure of pounds 4m.
John Clitheroe, a partner of Kingsley Napley, said that Mr Jones was unable to comment because of the legal situation. He added: 'All I can say is that there is an application for a judicial review in respect of the procedures which have been adopted.'Reuse content