Paul Cleeland, 49, who is in the 20th year of his sentence, said the Home Office had told a 'blatant lie' about the transcript.
His allegations came in an application for leave to challenge the Home Secretary's refusal to refer his case to the Court of Appeal.
Cleeland, who was convicted in 1973 of murdering a business associate, Terry Clarke, in Stevenage, Hertfordshire, says the transcript includes vital evidence from a defence witness.
Frank Lyne, then president of the Association of Public Analysts, told the jury that traces of lead found on Cleeland's clothing could not have come from a gun, according to Cleeland. However, this was not mentioned in the summing-up by the trial judge, Mr Justice Lane - now Lord Lane, the retired Lord Chief Justice.
In January, the Home Office had given assurances that it would use its 'best endeavours' to find a copy of Mr Lyne's evidence. However, earlier this month, Cleeland was told that no copies existed.
'That is a blatant lie by the Home Office,' Cleeland told Mr Justice Rose yesterday.
He said the transcript was attached to a secret report on his case produced by a senior police officer and held at the Home Office. At another High Court hearing before Mr Justice Popplewell last year, officials had accepted that the report was still in their possession, Cleeland said.
He had not drawn this to the court's attention before as he was afraid the Home Office would tamper with the documents.
Cleeland also criticised the Home Office for conducting internal inquiries into what he says was misleading evidence presented at his trial. An independent body should investigate, he said.
Mr Justice Rose refused leave for judicial review, saying there were no grounds to challenge the Home Secretary's ruling, but added: 'If it is the case that a transcript of the evidence of Mr Lyne is in existence, and more specifically was in existence last year when the application was made to Mr Justice Popplewell, clearly it is a matter of considerable importance that the Home Office says no such transcript exists. I shall direct that the terms of this judgment be brought to the attention of the Home Office in order for them to make such inquiry and give such explanation as they see fit in relation to this transcript.'