The offences were alleged to have taken place in a class and at library at a school between 1973 and 1977.
But after five days of legal argument without the jury, Judge Donagh McDonagh yesterday called back the seven women and five men on the panel to instruct them to issue verdicts of not guilty.
The nun threw her head into her hands and burst into tears at the back of Sligo Circuit Court after the judge delivered his ruling. She then hugged members of her legal team. One of the complainants in the case collapsed at the back of the court. Two others were helped from the room by relatives.
A fourth complainant sobbed loudly.
Judge McDonagh had ruled that the inconsistency of some of the evidence given by the complainants, made unsound by the passage of time, had made the trial unsafe.
Seven complainants had given evidence before the case was stopped a week ago to allow for legal arguments by the defence.
Some of them had claimed in court that the nun had told classmates 'Teigh a chodladh' -- Irish for 'go to sleep' -- before calling them to the front to her desk at the of the class where she indecently assaulted them.
Judge McDonagh said the claims had not been made in garda statements but "emerges mysteriously in evidence in court".
He said evidence given by some witnesses was "weak in certain aspects and tenuous in others".
The judge said he was struck that at no time did any of the complainants mention any events when they were in third class, like a school nativity play or First Communion.
"The passage of time has seriously affected the memories of the complainants," he said.
Judge McDonagh also addressed issues raised by the defence which alleged the complainants had colluded in their statements. He said: "I would hesitate to use the term collusion but there is a risk of cross-contamination when the events happened so long ago."