Kate and Gerry McCann ended up getting information from their own private investigators but refusing to share all of it with British detectives, according to the Home Office document obtained by Sky News.
The report, ordered by the then Labour Home Secretary Alan Johnson in late 2009, is believed to have said: “It is clear that the McCanns and the private investigators working on their behalf have gathered a large amount of information during the course of their enquiries.
“This information does not appear to have been shared fully with the Leicestershire Constabulary or the Portuguese authorities.
"It is imperative that they are encouraged and persuaded to share this information."
The report, written by the Child Exploitation and Online Protection Centre, adds: "Clearly, the McCanns have had a turbulent relationship with both Portuguese and UK law enforcement. They now openly acknowledge that there is a distinct lack of trust between all parties."
After Madeleine disappeared in Praia da Luz ten years ago, on May 3 2007, relations with Portugese Police soon became strained. Goncalo Amaral, the lead investigator in the case, was sacked in October 2007 after accusing British detectives of only chasing leads the McCanns wanted following.
In July 2008 he sparked a legal battle with the McCanns that continues to this day, by writing a book claiming the couple faked the abduction of their daughter after she died because of an accident in the holiday apartment.
Sky News’ account of the leaked report revealed how even before the book was published, the McCanns’ had felt the way some Portguese police officials treated them had been “inhumane”.
“It is clear,” the report states, “That from the beginning the McCanns felt there was a lack of clarity and communication on the part of the Portuguese police.
"Despite the involvement of British consular staff, they were, by their own accounts, left for long periods without any updates or communication with the investigators.
"They state they were taken to the police station on more than one occasion and then left for hours waiting to speak to someone who never materialised.
"They describe this situation as inhumane, with no real consideration for their emotional and physical wellbeing."
But, the report adds, relations with the UK authorities were also becoming strained.
Part of the problem, the report suggested, was that too many UK law enforcement agencies had rushed to help and caused chaos, while frequent criticism of the Portuguese investigation led to accusations that Britain was acting like "a colonial power".
The report recommended the creation of a UK national centre for missing children to better coordinate the response when British children go missing abroad.
Mr Johnson backed this recommendation, but it wasn’t implemented after Labour lost the 2010 General Election and the Conservative–Liberal Democrat coalition took power.
Mr Johnson told Sky News: “Nothing's happened in the ensuing 10 years that suggests that if it [a child disappearing abroad] happened again it would be an any better, more coordinated response."
The report, though, was one of the factors in the 2011 launch of Operation Grange, Scotland Yard’s review of the case.
The review, which is still ongoing, has so far spent £11m, with detectives having examined over 40,000 documents, leading to the generation of thousands of enquiries.
On 25 April, Metropolitan Police Assistant Commissioner Mark Rowley, the man in charge of Operation Grange, said his team continued to receive information on a daily basis and were still pursuing “a significant line of enquiry.”