Portuguese police believed Madeleine McCann died in her family's holiday flat and that her parents faked her abduction, a court heard yesterday.
Kate and Gerry McCann faced former detective Goncalo Amaral across a courtroom as he tried to overturn a ban on his book that claims their daughter is dead.
One senior detective told the hearing in Lisbon that police made the McCanns "arguidos", or suspects, in the case after concluding Madeleine died accidentally and her parents covered up the death by inventing a kidnapping.
Chief Inspector Tavares de Almeida said he believed Madeleine died in her family's apartment in the Algarve resort of Praia da Luz on the day she went missing.
He told the court the main evidence for this was the findings of British police sniffer dogs sent to Portugal to examine the flat.
The McCanns' lawyer, Isabel Duarte, challenged this claim, arguing that the sniffer dog results did not constitute proof.
Mr and Mrs McCann, both 41, from Rothley, Leicestershire, England, flew to Portugal yesterday ahead of the trial at Lisbon's main civil court, which is listed for three days.
Mr Amaral is calling a series of senior Portuguese officials involved in the investigation in to Madeleine's disappearance as witnesses.
His lawyers argue that the material in his book is contained in the official Portuguese police files for the case, many of which were made public in August 2008.
Jose Cunha de Magalhaes e Meneses, the local public prosecutor in the Madeleine investigation, gave evidence via video link.
Asked whether he believed that the little girl was dead, he said it was "50-50".
Mr Amaral's lawyers are also seeking evidence from a British policeman, Metropolitan Police Detective Sergeant Jose De Freitas, who was seconded to Leicestershire Police to help with the British end of the investigation.
Mr and Mrs McCann are not expected to give evidence.
Madeleine was nearly four when she went missing from her family's apartment in Praia da Luz on May 3, 2007.
Mr and Mrs McCann were made "arguidos" four months later, but this was lifted when the investigation was shelved in July 2008.
The couple have always strenuously denied having any involvement in the disappearance of their daughter, whom they believe was abducted.
Mr Amaral at first led the Madeleine inquiry for Portugal's CID, the Policia Judiciaria.
But he was taken off the case in October 2007 after criticising the British police in a newspaper interview.
In his book 'Maddie: The Truth Of The Lie', published in July 2008, Mr Amaral claimed that Madeleine died in her family's holiday flat on the night she vanished and questioned the McCanns' account that she was abducted.
A Portuguese judge granted the McCanns an injunction in September last year banning further sale or publication of the book. The former policeman was also prohibited from repeating his claims.
The McCanns sat just yards away from Mr Amaral at the front of the public gallery in Lisbon's 7th Civil Court.
They occasionally whispered to each other and their Portuguese translators, but made little reaction to what was said.
A spokeswoman for the couple said that sitting through the allegations made in yesterday's hearing was painful for the couple.
The McCanns are also seeking €1.2m in compensation for defamation in separate legal proceedings against Mr Amaral.