Lawyers working for the Tanaiste, Ms Harney, were advising her to appeal yesterday's decision of the High Court within hours of it being handed down.
The appeal papers to the Supreme Court must be lodged within three weeks and work has already begun.
While the ruling handed down yesterday may have surprised the Department, both sides in this mammoth battle have known that whatever the outcome, a trip to the Supreme Court was inevitable.
It is likely to be some time later this year before this matter is concluded although the potential for it to rumble on into next year cannot be ruled out.
The delay created by the three High Court and one Supreme Court hearings which have already occurred, may itself become an issue.
One reason for Mr Justice Butler's decision yesterday was that authorised officers can be appointed to companies where there is a suspicion of unlawful activity, but not where there is "illegality of an historical kind".
Many of the concerns expressed by Ms Harney about the Dunnes companies relate to the years when Mr Ben Dunne was at the helm.
Mr Dunne resigned from his executive role in 1993.
Should the Supreme Court not change Mr Justice Butler's ruling, it could have repercussions for the section of the Companies Act 1990 under which authorised officers are appointed.
Under the law appointments can be made if there are "circumstances suggesting" it is "necessary" to investigate the company to establish whether various improper matters may have occurred.
The Minister need only be "of the opinion" that such circumstances exist, though it follows from what has transpired to date in the Dunnes saga that companies can in future seek to be given the reasons why the Minister formed an opinion.
Mr Justice Butler, as another of his grounds for his decision yesterday, said there was "no evidence" that it was necessary to have the Dunnes books examined.
How this fits in with the Minister, under the law, having only to form an "opinion" is not immediately clear.
It also seems from the judgment that the court has ruled that as long as the persons affected by alleged illegalities have not complained, the Minister cannot appoint an officer to investigate a case where he or she suspects one shareholder of a company has defrauded fellow shareholders.
The Department may consider this to be an unsatisfactory position.
It is hard to see how the ruling will have any effect on the various authorised officers' inquiries currently under way. Ms Harney has put a rash of inquiries in train in the wake of the McCracken Report.
The companies to which authorised officers have been appointed include: Guinness & Mahon Bank; Irish Intercontinental Bank; Ansbacher Cayman Ltd; Hamilton Ross Ltd; Celtic Helicopters; Garuda Ltd; and Faxhill Homes Ltd.
Many of these inquiries have been completed, the most recent being that into Irish Intercontinental Bank. The Tanaiste is currently considering whether, on foot of the authorised officer's report, she should seek the appointment of a High Court inspector.
Such a move has already been made regarding Ansbacher Cayman Ltd.
Ms Harney is to introduce legislation in the autumn which will establish the office of the Director of Corporate Law Enforcement.
This office will take responsibility for the appointment of authorised officers, seeking the appointment of High Court inspectors, thereby taking the issue out of the political domain.
The level of supervision of company law seen during Ms Harney's tenure in the Department of Enterprise, Trade and Employment, may continue after she has moved on.