A dossier of fresh allegations allegedly involving other senior Tory figures was sent to Sir Gordon Downey, the Parliamentary Ombudsman, by Mohamed al-Fayed, the owner of Harrods.
His claims that he had paid thousands of pounds in cash in envelopes to Mr Hamilton led to the libel action.
The Prime Minister's office faced calls for the papers to be submitted to a fresh investigation of Mr Hamilton by a Commons committee of MPs. Downing Street is resisting pressure to publish the documents, which led to the case being dropped.
They showed a conflict between Mr Hamilton and Ian Greer, the head of a public relations company who was also suing The Guardian. The newspaper, which received the government documents, said the Inland Revenue would find "much to interest them".
Alex Carlile, the Liberal Democrat MP, told The Independent that he is writing to Sir Gordon to call for him to investigate complaints he had made alleging Mr Hamilton received pounds 25,000 in cash and vouchers.
There was growing pressure last night for Sir Gordon to be given tougher powers.
The newly created select committee on standards in public life is dominated by Tory MPs who could frustrate an inquiry until after the election.
Lord Nolan, who reported on standards in public life, warned that Parliament was being damaged by the allegations of sleaze; these, he said,should be investigated by Sir Gordon. Sir Gordon replied: "the judicial system has opportunities which are really open to a select committee inquiry or an inquiry by me."
Donald Dewar, the Labour Chief Whip, led demands for a thorough investigation by Sir Gordon.
He said: "In the interests of the public, we have got to get to the bottom of it. I hope Sir Gordon Downey will call for persons and papers will get all the raw material so that we can make a proper judgement."
Labour is likely to press for a debate immediately the Commons returns on 14 October. Mr Hamilton said he is referring the affair to Sir Gordon to clear his name.
Mr Dewar said: "I am not sure that will be popular with some of his own colleagues allegedly involved in the affair but there clearly is a need to properly investigate it."
There was also anger among Labour MPs over a vote in the House of Lords for a change in a 300-year-old law which enabled Mr Hamilton to pursue his case.
A Labour MP, Denis MacShane, wrote to Commons Speaker Betty Boothroyd calling for an urgent debate over how parliamentary rules were changed "to benefit Mr NeilHamilton" in his libel action. The Conservative Party insisted it was "a matter between Mr Hamilton and TheGuardian.Reuse content