In an e-mail dated 3 September, 2007, John Lowe, of the major incidents team at the Birmingham-based Forensic Science Service (FSS), said it was impossible to conclude whether or not the material came from the couple's daughter, Madeleine.
Four days later, Portuguese detectives named the McCanns arguidos – formal suspects – in the child's disappearance, citing DNA evidence as grounds for their suspicions.
The revelation came to light after the police files from the inquiry, which lasted more than 14 months, were formally made public.
Journalists were handed DVDs containing copies of thousands of pages of evidence from the case outside the courthouse in the Algarve town of Portimao.
The dossier includes details of the lines of inquiry pursued by detectives, forensic reports, witness statements and transcripts of interviews with the McCanns, both 40, from Rothley, Leicestershire.
Among the files is the e-mail written by Mr Lowe to Detective Superintendent Stuart Prior, the head of the British side of the investigation.
In it, the scientist reported that a sample from the boot of the Renault Scenic car, which the McCanns rented 24 days after Madeleine went missing, contained 15 out of 19 of her DNA components.
But he cautioned that this result – based on the controversial "low copy number" DNA analysis technique, which uses very small samples – was "too complex for meaningful interpretation or inclusion".
Mr Lowe wrote: "Let's look at the question that is being asked: 'Is there DNA from Madeleine on the swab?'
"It would be very simple to say 'yes', simply because of the number of components within the result that are also in her reference sample.
"What we need to consider, as scientists, is whether the match is genuine – because Madeleine has deposited DNA as a result of being in the car, or whether Madeleine merely appears to match the result by chance."
The expert noted the components of her DNA profile were not unique – in fact some of them were present among FSS scientists, including him.
He concluded: "We cannot answer the question: 'Is the match genuine, or is it a chance match?'"
Mr Lowe also stressed that low copy number analysis could not determine when or how the DNA was deposited, what body fluid it came from and whether a crime had been committed.
The e-mail was translated into Portuguese on 4 September, 2007, the documents revealed.
The police files were released under Portuguese law after the lifting of the period of judicial secrecy in the case.
Lawyers for the McCanns were formally given access to the documents last week. Their official spokesman said they would not be commenting about the newly-released files.
The police files also reveal detectives categorically told Mr McCann in interview that Madeleine's DNA had been found in the hire car. A friend of Mr McCann said it seemed clear that the Portuguese police were trying to extract a confession from him. The friend added: "It would appear they were seeking to apply pressure by overstating the evidence that they had – and frankly it is a scandal."
Although the questioning on 7 September last year was not recorded, an unidentified police officer took notes, which were included in the dossier.
The officer wrote that Mr McCann was told his daughter's DNA was discovered in the boot of the rented Renault Scenic and behind a sofa in the family's holiday apartment.
The notes said: "Confronted with the fact that Madeleine's DNA was gathered from behind the sofa and from the boot of the vehicle, and analysed by a British laboratory, he said he could not explain why this would be."
This contradicts the FSS expert's opinion that the sample found in the car could not be definitively linked to the little girl. Clarence Mitchell, the McCann family's spokesman, said: "I can confirm that the Portuguese police put it to Gerry as a fact that Madeleine's DNA had been found in the apartment and the vehicle, when it is now clear that that was not the case, and that the initial FSS report had said the findings were inconclusive.
"You have to ask what the police were trying to achieve by over-presenting evidence that they did not have, and clearly could not claim to have."
Madeleine was nearly four when she vanished from the holiday apartment in the Algarve on 3 May last year, as her parents dined with friends nearby.
Despite a huge police investigation and massive coverage in the Portuguese and British media, the little girl has not been found.
On 21 July, Portuguese prosecutors announced that they were shelving the case.
Mother silent through barrage of questions on disappearance
KATE McCann refused to answer 48 questions put to her by Portuguese detectives after she was made a suspect in Madeleine's disappearance, the police files reveal.
She used her right as an arguido, or formal suspect, to remain silent during this section of her interview on 7 September last year.
Officers quizzed her about everything from her medical specialism and Madeleine's behaviour to whether she had any responsibility for the little girl vanishing.
Detectives started by asking Mrs McCann about her movements immediately after she discovered that her daughter was missing at about 10pm on 3 May last year, a document in the massive police dossier shows.
She was asked where she looked, what she touched and whether she searched inside the wardrobe that was in the master bedroom.
The questioning turned to the raising of the alarm and the involvement of the media.
Officers asked Mrs McCann general questions about her relationship with her children and her work.
The 40th question was: "Is it true that sometimes you despaired with your children's behaviour and that left you feeling very uneasy?"
It was followed by: "Is it true that in England you even considered handing over Madeleine's custody to a relative?"
Mrs McCann was also invited to comment on the evidence of sniffer dogs and DNA testing on samples taken from the McCanns' holiday apartment and hire car.
The final unanswered question was: "Did you have any responsibility or intervention in your daughter's disappearance?"
The files show that the only question Mrs McCann did answer was: "Are you aware that in not answering the questions you are jeopardising the investigation, which seeks to discover what happened to your daughter?"
This time she replied: "Yes, if that's what the investigation thinks."
Mrs McCann has always strenuously denied any involvement in Madeleine's disappearance. Her arguido status, and that of her husband Gerry, was lifted on 21 July.
Sad images of loss in police file
MADELEINE McCann's bed, empty apart from her treasured Cuddle Cat toy, hours after she vanished were among the dramatic images contained in the file. Pictures in the dossier show the inside of the apartment where Madeleine McCann is believed to have been snatched.
The bed, which has been made, is next to a play pen.
On it lays the pink toy left behind by the child. Kate McCann was often seen carrying the stuffed toy for support during the months following Madeleine's disappearance on 3 May last year.
Other photos show the view from the apartment's balcony which looks on to the tapas bar at which the McCanns dined with friends on the evening their daughter went missing.