Justice for the 270 victims of the Lockerbie bombing was placed in doubt again last night after the conviction of a former Libyan intelligence agent was seriously undermined by a new ruling.

The Scottish Criminal Cases Review Commission said there were no fewer than six grounds on which Abdelbaset Ali Mohmed al Megrahi may have suffered a miscarriage of justice, and granted him leave to launch a second appeal.

Its verdict, after a three-year investigation, proved highly embarrassing for the Crown Office team which brought the case against Megrahi seven years ago, and for the judges who decided his guilt at the trial and first appeal in the Netherlands.

Despite Megrahi's conviction, there have been persistent claims that Libya was not responsible, that some evidence was rigged, and that the finger of suspicion pointed elsewhere - in particular to Palestinian terrorist groups.

The commission rejected allegations that evidence had been falsified or "spirited away" by the investigating teams but the defence insists responsibility lies elsewhere.

New evidence unearthed by the commission is thought to include a paper trail implicating Iran but, because Abu Talb, a member of a Palestinian organisation backed by Iran, appeared as a witness at the Camp Zeist trial, he received Crown immunity from future prosecution.

The commission also concluded yesterday new evidence about the unreliability of key witnesses, and the non-disclosure to the defence of important and classified information, were strong grounds to refer the case back.

Sir Oliver Miles, former British ambassador to Libya, said he doubted whether the full facts of Lockerbie would ever be known. He told the BBC: "No court is likely to get to the truth, now that various intelligence agencies have had the opportunity to corrupt the evidence."

Some relatives of Lockerbie victims welcomed the decision, saying they believed Megrahi was probably innocent, based on the evidence presented at his trial.

Dr Jim Swire, whose daughter Flora was one of the victims, said: "It's no good trying to have closure on false foundations if they are false. A house built on sand cannot stand."

But some American families were disappointed. Daniel Cohen of New Jersey, who lost his 20-year-old daughter, Theodora, said: "Nothing brings your child back, but you really want to have a clear record for history of what happened here."

Megrahi himself, now 55, who is serving his life sentence at Greenock Prison, welcomed the decision. In a statement issued through his solicitor, Tony Kelly, he said: "To the relatives of those many people who died on December 21 1988, I can say very little that will not sound insensitive. What I would like to reiterate, however, is that their cause is in no way served by the incarceration of an innocent man. Like them, I wish the whole truth about PanAm 103 to be exposed."

Mr Kelly said an application may be submitted to request bail for Megrahi. "This is just the start. The commission has not come to its decision lightly: this is a matter of some moment, not only to Megrahi, but to the Scottish criminal justice system."

The Crown would strongly oppose an application for bail pending the appeal.

Mohammed Elzwi, a Libyan official dealing with the Lockerbie issue and former ambassador to the UK, said of the new appeal: "The decision opens the door of hope regarding the innocence of Megrahi. This decision will have good consequences."

Alex Salmond, the First Minister, said it was "in the interests of justice" that the case go back to court. "We must allow the independent legal process to take its course. Let us never forget that 270 men, women and children lost their lives in December 1988," he added.

The case will now go before five appeal judges, at a sitting likely to take place in Edinburgh next year. It presents a serious logistical problem because so many of the country's current judges were involved, either on the bench or as prosecutors, in the original trial and appeal.

Lord Hamilton, the current Lord President and Scotland's most senior judge, yesterday called on the executive to appoint additional judges to help cope with the shortfall.