Frank Mulholland, QC, the Solicitor-General for Scotland, said his heart went out to Alan Mackay, who "disappeared" on Monday and failed to attend court as the trial judge announced he was ending the case because of a lack of evidence against Angus Sinclair.
Mr Mulholland's comments to The Scotsman came as Elish Angiolini, the Lord Advocate, announced she would make a statement to MSPs tomorrow defending the Crown Office's position in the case.
Ms Angiolini agreed to make a statement to the Scottish Parliament after mounting pressure from opposition politicians yesterday. They were angered over the extraordinary collapse of the case against Sinclair, who was charged with raping and murdering two 17-year-old girls after they visited the World's End pub in Edinburgh 30 years ago.
Mr Mackay had chosen not to lead evidence which, although weak, might have linked Sinclair with one of the ligatures used to strangle Helen Scott and Christine Eadie. It is understood he believed there was sufficient other, and stronger evidence, to entitle the case to be put before the jury.
Police announced yesterday that they were satisfied as to the whereabouts and well-being of Mr Mackay.
Observers believed that the Crown would dispute Lord Clarke's judgment, although there is no right of appeal against it.
Mr Mulholland, the law officer whose post is second to the Lord Advocate in the hierarchy of the prosecution service, told The Scotsman: "My heart goes out to Alan. He is a fantastic prosecutor. He is competent, he is able and he is highly regarded by his peers and by the judiciary.
"Everyone knows how hard he took the decision in this case. No-one feels more gutted than Alan Mackay at the outcome of the case."
Asked if he would defend Mr Mackay's decision on the DNA ligature evidence, Mr Mulholland added: "I do defend his decision. It is a call he made, and it was a call for very good reasons and I can understand his reasons for doing it. I fully back him in his decision-making. We just want him back safe and well."
Mr Mulholland revealed that he was last night to meet the senior investigating police officer in the case.
"I want to personally thank him for the efforts he has put in and the efforts of his team, and to assure him that the outcome is no reflection on the work of his team. Like them, we are hugely disappointed at the result of the case."
Police in Glasgow also played down speculation that they were unhappy about the way the Crown Office handled the case against Sinclair.
There have been reports that detectives from Strathclyde Police also wanted the Crown to charge Sinclair with the murders of Anna Kenny and Hilda McAuley in Glasgow, and Agnes Cooney in nearby Coatbridge, which happened in the same year as the World's End murders.
But the force's Assistant Chief Constable John Malcolm said: "Strathclyde Police would wish to set the record straight.
"The views expressed in the media by any unnamed 'police source' or 'police officer' are not the views held by Strathclyde Police."