The case is reported to have been fallen apart on the grounds that there were flaws in its construction.
However, state prosecutor Jón Snorrason said he would appeal against the decision to clear chief executive Jóhannesson and five other defendants on 40 separate counts of fraud and embezzlement.
Jóhannesson had been accused of providing illegal loans to Baugur from his personal investment company, Gaumur.
His involvement in the case prevented Baugur making a joint bid for grocer Somerfield, although last week Baugur did increase its stake in fashion group French Connection, prompting speculation that it may try and buy the retailer.
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