James Wolffe QC said the case against David Whitehouse and Paul Clark was a “very serious failure” in the prosecution system.

The experts were appointed when the company went into administration in 2012 but were arrested and embroiled in a legal nightmare before the charges against them were dropped.

The Crown has admitted their prosecution was malicious and that the men have been awarded £10.5 million each in damages.

Opposition politicians have called for an independent public inquiry.

Mr Wolffe gave an “unreserved apology” to Mr Whitehouse and Mr Clark, saying they should not have been prosecuted.

He added: “In this particular case there was a very serious failure in the system of prosecution.

“It did not live up to the standards I expect, which the public and this parliament are entitled to expect, and which the Crown Office expects of itself.

“What happened in this particular case should not have happened, I tender my apology to the Parliament and the public that it did happen, and for the consequent cost to the public purse.”

He claimed, however, there had been no criminal misconduct in the Crown Office’s investigation.

Mr Whitehouse issued a statement saying those in the Crown Office who took the decisions against him and Mr Clark “should be held accountable”.

“I firmly believe that a criminal investigation is justified.”

Scottish Conservative finance spokesman Murdo Fraser said: “Not only will this end up costing taxpayers tens of millions of pounds at a time when our police and courts are in desperate need of resources, but it raises fundamental questions about integrity.

“This was not simple human error or an obscure legal mistake. Our prosecution service has admitted that, acting with malice, they sought to throw innocent men behind bars and destroy their reputations.”

Labour justice spokeswoman Rhoda Grant said: “The Lord Advocate says that the system has been improved, but there cannot be proper scrutiny of this until we know exactly what went wrong in the first place.

“Until this happens, how can he expect to restore confidence in the system?”

Scottish Green MSP John Finnie said: “The Lord Advocate must commit to undertaking the considerable work required to restore public confidence in Scotland’s justice system.

“The checks and balances cited by the lord advocate as reasons people can have faith in the system seem to have been completely bypassed in this appalling situation.”

Scottish Liberal Democrat MSP Liam McArthur said: “This is a true scandal of monumental monetary terms.”

He also called for “a full, independent and judge-led inquiry”.