Last Sunday, a solitary figured stood outside the home of Robert Murat, the Englishman questioned in the Madeleine McCann case, as police forensic experts searched the villa.

A week on, searching questions are being asked about why Guilhermino da Encarnacao, the chief investigating officer, switched the focus of his inquiries on to one man. Even the police admit there is, to date, no credible evidence against Murat.

Described as a “desk strategist”, Encarnacao, a methodical 59-year-old officer, now heads one of the most intensively scrutinised police investigations in recent history.

There are questions over the resources and time spent investigating Murat. It has also emerged that Encarnacao was involved in a previous investigation of a missing child, which was hit by criticism.

“As police we can’t make miracles happen,” he has said in one his few interviews. “Let’s hope God will allow us to solve the case.”

There were no miracles last week and after 17 days, Madeleine is still missing. The trauma consultants with the McCann family have gently helped them to at least consider the possibility that their daughter is now dead, although the couple are convinced she is still alive.

Police are widening their inquiry, with new searches in other European countries and northern Africa.

A report of a small child matching Madeleine’s description in Marrakesh on May 9 was yesterday reported to have been discounted.

The profile of the case remains as high as ever. A two-minute appeal was shown on the big screen at Wembley ahead of the Manchester United-Chelsea FA Cup Final. The website appealing for help has had more than 60m hits.

The results of forensic tests on Murat’s property are still awaited, but the questions are being asked: what was the evidence that initially made him a suspect? Were searches of properties connected to him conducted effectively? And why was he still allowed to attend witness interviews as a police translator while under suspicion?

Last week it emerged that Encarnacao was also involved in another high-profile missing child case when Joana Cipriano disappeared from her home in the village of Figueira on September 12, 2004, only seven miles from the coastal resort of Praia da Luz where Madeleine went missing on May 3.

In echoes of the McCann case, the hunt for Cipriano got off to a false start when the Republican National Guard, another police body, failed to seal off the house where Joana was last seen. It was only five days later – after hundreds of police officers, journalists and friends of the family had trampled over the scene, and after relatives had cleaned the house with bleach – that the Judicial Police took over.

Joana’s body was never found, but the case was solved. Leonor and Joao Cipriano, her mother and uncle, were convicted of killing Joana and sentenced to 16 years and eight months, but they never confessed.

The inquiry into Murat, 33, has appeared haphazard at times. The search of Murat’s villa last week was carried out in the presence of Murat himself, his mother and the latter’s dogs. “You’d think the police would clear the villa while conducting a forensic search. Instead members of the family were allowed to come and go as they liked,” one source who witnessed the search said.

The home of Sergey Malinka, 22, a Russian who helped Murat set up a website for his estate agency, was searched a day after Murat’s villa. “If there was anything on Malinka’s computer, he would have had plenty of time to erase it,” a source close to the investigation said.

Not even credible circumstantial evidence has been made public against Murat. It has been reported that he phoned Malinka on the night of the abduction, despite the Russian previously claiming to reporters that they were not friends and had not seen each other for months.

Malinka would not comment on the calls yesterday, but it was perhaps not surprising if he did play down his links to Murat to avoid unwelcome attention. He is said to be considering legal action over reports that he had criminal convictions for sex offences.

He said this weekend: “If you were called a paedophile in the papers, what would you do? The disappearance of the child is horrible, but when you become the centre of the world’s attention like this it is very unpleasant. I am innocent. I have a clean conscience. It is a terrible tragedy and I hope they find her.”

Questions were also raised last week why Murat hired a rental car at short notice two days before he was taken in for questioning. Sally Everleigh, Murat’s cousin, said: “There’s nothing suspicious about it at all. He hired the car so that he could go to Portimao to help police to translate. It wasn’t a getaway car or anything like that. He was just trying to be helpful.”

The estranged wife of Murat also spoke out this weekend in his defence. Dawn Murat, who lives in Hockering, near Dereham in Norfolk, said: “There is no doubt in my mind he is innocent. He loves children and is the most kind and generous person I have ever met.

“I feel for him deeply. I am disgusted at what people are saying. It is just total shock and disbelief. I feel he has been made a scapegoat. He is not capable of hurting anybody.”

Murat hopes his phone records will help to prove his alibi on the evening of the abduction. It is understood he twice phoned England and spoke to his daughter.

It emerged last week that Murat was involved in the hunt for Madeleine from the first day. A resident close to the McCanns’ flat, who knows Murat and his mother, said he had helped the police to search her property. “Murat took part in the search of my flat. He went into my spare bedroom and looked under the bed,” she said.

A senior officer said: “He offered himself as a translator to the police and in the beginning there were no suspicions of him. Last Saturday he was used as a translator in Portimao when police interviewed a witness. At that time we already had suspicions so we didn’t use him to do important interviews. But we thought if we said that we didn’t need him it would be worse because it could alert him.”

One source said: “The senior officers in this case have been sleeping just an hour or two every night. They were all fired up when they started the search at Murat’s villa, but they’re not any more. What they’re looking for is someone or something to link Murat to Madeleine.” Other leads are thin on the ground.

Tax blow for search fund

In addition, the fund will not benefit from gift aid, a form of tax relief that allows charities to claim from the government an additional 28p for every £1 they receive in donations. And tax will have to be paid on all interest accrued by the fund.

Last night the Treasury refused to intervene, insisting it was the preserve of HM Revenue & Customs to decide tax liability.

The development will embarrass Gordon Brown who told Madeleine’s family last week he would do all he could to help on “a practical and a personal level”.

The decision on charitable status could hit the family’s efforts to trace Madeleine. Her parents Kate and Gerry are considering hiring a private investigator amid concern over the way police have handled the hunt. A FUND to finance the international search for Madeleine McCann will be forced to pay Vat and denied tax breaks worth tens of thousands of pounds after being refused charitable status writes Mark Macaskill.

The Madeleine fund has already received almost £80,000 from the public and businesses. Madeleine’s parents had hoped for charity status for the fund but were turned down by the Charity Commission because the money raised is not for the “wider public good”.

Instead, the fund has been registered as a company, which means it is liable to pay Vat at 17.5% on advertising costs and goods designed to raise funds, such as stickers. Charities are eligible for “zero rate” tax relief on such expenses.

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