World football's governing body said this month it had been forced to delay the publication of the potentially incriminating documents following objections from one of the parties involved.
But FIFA President Sepp Blatter also said he remained determined the documents would be published as part of his plan to clean up his organisation, which has been plagued by allegations of corruption.
FIFA said in a statement on Tuesday it would not appeal against the court decision "as it corresponds to the position of FIFA and its President, Joseph S. Blatter, to open the ISL/ISMM case file."
The court decision was reported by the Swiss consumer magazine Beobachter on its website.
A court spokesman confirmed that a decision had been reached but declined to give any further details.
Blatter announced in October that he wanted to reopen the case into the collapse of ISL, which went bankrupt in 2001.
Swiss prosecutors investigated the collapse of ISL but the case was settled after they said two FIFA officials - whose names have not been divulged - paid back 5.5 million Swiss francs ($6.1 million).
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