The judge was highly critical of the Office of the Director of Corporate Enforcement
The Taoiseach Enda Kenny has ordered a full report into Ireland’s corporate affairs watchdog in the wake of Sean Fitzpatrick's trial collapsing.
Mr Kenny said it is "not good enough" that the Office of the Director of Corporate Enforcement (ODCE) appeared not to request further resources for its case.
Opposition parties have complained today after the agency said limited resources had affected its ability to take the case.
He said he has asked for a full report into how the office is set up and run.
"We can’t have a situation where an independent statutory agency - that does not take legal advice from the Office of the Attorney General, that proceeds on its own, that looks for resources from the Department of Jobs and Enterprise - and that this trial collapsed here," he said.
"We know why the first trial collapsed and we have the condemnation of a judge yesterday, who has said that this case could not proceed any further."
The Jobs Minister Mary Mitchell O'Connor is to receive the report.
The ODCE say the report will be prepared "as a matter of the highest priority."
In a statement, the ODCE says: "On foot of various directions given by the trial judge, ODCE personnel were excluded from large portions of the trial.
"Consequently, the ODCE is not at this time in possession of complete information as regards all aspects of the trial, including legal arguments made by the prosecution and defence, or the resultant rulings delivered by the judge."
The ODCE confirms it has requested full transcripts of the trial from the Director of Public Prosecutions (DPP).
Mr Fitzpatrick was formally acquitted in front of a jury at the Dublin Circuit Criminal Court on Wednesday morning.
The case collapsed on Tuesday following a ruling by trial judge Martin Aylmer that it should not go to the jury because of the shortcomings in the prosecution's evidence.
The judge was highly critical of the investigation by the ODCE.
The former CEO of Anglo Irish Bank had been accused of misleading the bank’s auditors Ernst & Young and of furnishing them with false information in relation to multi-million euro loans.
During the trial, the court heard the two main prosecution witnesses had been "coached" and Judge Aylmer expressed his concerns about the level of contamination and cross-contamination in their evidence.
He was also highly critical of ODCE lead investigator Kevin O’Connell for the shredding of certain documents.
Today, he told the jury that the investigation fell short of that which an accused person should be entitled to.
He described the prosecution’s case as "insufficient" and directed the jury to acquit Mr Fitzpatrick of all 27 charges. The court heard nine of those charges had already been dropped by the DPP.
Judge Aylmer thanked the jurors for their attendance and attention over the past eight months before excusing them from service for life.
He then told the former CEO of Anglo Irish Bank he was "now free to go" – to which Mr Fitzpatrick replied: "Thank you Judge."
The court heard there are no further outstanding prosecutions against him.
Mr Fitzpatrick emerged from the Criminal Courts of Justice to a sea of photographers, reporters and TV crews as he made his way to a waiting taxi.
He left the building hand in hand with his daughter before getting into a waiting taxi.
At 127 days, today marks the end of the longest criminal trial in the history of the State.