Ministers announced the move after a judge at Liverpool Crown Court called for an inquiry over a range of allegations about investigators' behaviour which were put to a pre-trial hearing.

Ten weeks into the hearing the prosecution decided against offering further evidence and the 15 defendants walked free.

Scotland Yard's specialist crime unit has already launched its own inquiry into possible criminal offences connected with the alcohol investigations, according to The Guardian newspaper.

Obviously there are going to be high profile cases where things go wrong - and this was one

Customs chairman Richard Broadbent

It says the collapsed investigation and trial are estimated to have cost the taxpayer �30m - on top of more than �1.25bn in lost revenue to the exchequer.

Now the minister responsible for customs, economic secretary to the treasury John Healey, and the minister responsible for customs prosecutions, attorney general Lord Goldsmith QC, have set up an independent review to be conducted by a high court judge.

Customs and Excise chairman Richard Broadbent told The Guardian the review would be "uncomfortable".

But he said it was important "issues arising from complex investigations into serious crime are examined".

Mr Broadbent told the paper: "A public body should be open to public scrutiny.

"While it would be foolish to say that in an organisation of 25,000 people there are no bad apples, I am satisfied that there is no endemic or systematic corruption."

The flagrant disregard for the law which customs has displayed has led to the unnecessary loss of hundreds of millions of pounds of public funds

Defence solicitor Lesley Burrows

Mr Broadbent added: "Obviously, there are going to be high profile cases where things go wrong - and this was one.

"In the Liverpool case we had 32 QCs representing the defendants raising questions - each capable of finding evidence of where the process had gone wrong."

He said: "Much has changed in customs over recent years.

"There is more to be done - but I welcome an authoritative and independent audit of the situation at this stage."

Customs and Excise handles about a quarter of serious criminal cases in the UK.

But solicitor Matthew Frankland, whose firm Decherts represented four men, told The Guardian the hearing "should be the catalyst for customs and excise being stripped of their power to prosecute".