A number of police officers are under investigation after allegations that they stole cash or other valuables during an unprecedented police raid on more than 3,000 safe deposit boxes in three security vaults in London last year, The Independent has learnt.

Scotland Yard's professional standards directorate is investigating nine complaints, include two allegations of theft, against police officers who took part in Operation Rize, the raid on three security vaults beneath some of London's most select neighbourhoods.

It was claimed at the time that the operation, in which some officers were heavily armed, had uncovered an "Aladdin's cave" of criminal proceeds worth at least £35m.

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However Scotland Yard's internal investigation comes amid wider concerns that the raids trampled on the privacy of 2,500 innocent box holders, who include a Holocaust survivor and High Court judges. Each holder of the 3,554 boxes seized last June at the depositories operated by Safe Deposit Centres Ltd has had to prove they legitimately own items and cash found in the boxes, or face a criminal investigation. Lawyers say the raid has set a disturbing precedent for indiscriminate "fishing trips" by police seeking evidence of wrongdoing.

Detectives from the Yard's Economic and Specialist Crime Directorate insist Rize has been a substantial success, leading to 40 arrests for offences ranging from running prostitution rings, money laundering, drug supply, paedophilia, burglary and benefit fraud. Eleven prosecutions have been brought in connection with this raid, they say.

But an investigation by The Independent has revealed that nine complaints have been made against officers who took part in the raid, including two separate claims of theft: it has been alleged that small items of jewellery and £8,500 in cash were removed from boxes. Three claims for compensation arising from damage to property caused by police, understood to total around £5,000, are also being processed.

The Independent understands that among the unwitting box-holders caught up in Rize was a Jewish man who survived the Holocaust as a child. He kept a lump sum in case his family ever needed to flee their home once more. A father whose daughter was killed in a car accident had placed the cash compensation he received in a security box because he did not know what to do with it. Another family was using a box to store money that a relative with a gambling addiction had "paid back" after years of theft.

Several High Court judges and senior police officers, as well as a well-known businessman and a scion of an international banking family were also clients of Safe Deposit Centres. Some of the boxes held highly personal possessions, such as photographs and details of second families. The contents of about 2,500 boxes have now been returned to customers while around 700, containing up to £15m in cash, have been passed to HM Revenue and Customs to be investigated for tax evasion.

Cash has only been returned after owners were able to provide documents proving its source and that any taxes due on the sum have been paid.

When Roger Mortlock, 59, had his box returned to him after an exhaustive verification process for the £110,000 he had stored, he said it contained £8,500 less than it had the last time he counted the cash.

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Mr Mortlock, who is being treated for cancer, said: "I got the box because we had been burgled twice. Having a box doesn't make you a criminal.

"I couldn't believe the way I was treated. I felt as if I was guilty until I had proved myself innocent. It took months to even get to the stage where I was allowed to retrieve my belongings, and then I found that a substantial amount of the money had gone missing."

Jeffrey Lewis, senior partner of law firm Lewis Nedas, which has represented more than 70 box-holders, said: "If police want to search a flat rented by a drugs dealer in a block of flats, they would ordinarily be granted a warrant to search the flat used by that particular suspect. In this case, they have in effect smashed their way into every flat on no real credible basis."

Lawrence Kelly, partner at Lawrence Stephens Solicitors, which has also represented box-holders, said: "What police seem to have achieved is to search and seize first, and then place the onus on the individual to prove they have acted lawfully."

Detectives leading Operation Rize said they had reason to believe a "high percentage" of the boxes were being used by criminal gangs. They admitted "innocent" box-holders had been inconvenienced by the investigation but underlined that the operation had scored significant success in targeting serious criminals.

A Metropolitan Police spokesman said: "A priority for the investigation has been to ensure that where contents are held legitimately, the owners have the contents returned to them as soon as possible."