The 440-pupil school, which serves the island of Bute, was awarded 16 fairs and three unsatisfactories by inspectors, who classed nothing as good or very good in one of the harshest recent condemnations of a secondary.
Peter Peacock immediately intervened, dispatching a letter to Allan Macaskill, leader of the council, stating: "The school clearly needs a radical transformation and my immediate concern, which I am sure you share, is that the situation in Rothesay Academy is improved rapidly.
"I would like to know what actions you are taking, what you plan to achieve and in what timescales. But I am also concerned about how the unsatisfactory situation at Rothesay Academy which has been revealed by the inspection report was not identified through the council's own processes and addressed by the council at an earlier stage.
"I would like your reassurance that you have in place procedures that enable you to assess school performance and take appropriate and timely action."
In a final barb, Mr Peacock reminds Mr Macaskill that the council's education department is due to be inspected. "I will be particularly interested to see its outcome in due course," he states.
The backdrop to ministerial concern is the new legislation to provide extra powers to intervene in failing schools and authorities. Councils contend that this measure is unnecessary.
In a statement, Argyll and Bute replied that it has a well-established and constructive relationship with the inspectorate and "it has been the council's practice to give full attention to HMIE reports".
It adds: "The council is well placed to do this. Following restructuring in 2003, community services - the department which includes the former education department - has put into place an enhanced quality improvement team specifically targeted on secondary education.
"This team will provide significant additional support to the school over the next two years in achieving the improvements required."
The authority is appointing a new headteacher and intends to rebuild the school before 2007.
Disruptive behaviour among a significant minority of pupils contributed to Rothesay's downfall and poor standing in the community. Many parents told inspectors they were dissatisfied.
HMI criticised low levels of attainment, ineffective teamwork and poor learning and teaching in some classes.
Stewart Shaw has been acting head since last November when Andy Gilmour was drafted into the council to head its post-McCrone implementation plans.
Inspectors do not hold back. "The acting headteacher was having to take the school forward from a position where major weaknesses in leadership in the past had left the school with these significant failings," they state.
Most staff thought the school was well led but a significant number of parents disagreed.
"Overall," inspectors say, "the work of senior managers lacked consistency, rigour and challenge and this resulted in them having little overall impact."
Most pupils were well behaved and co-operative but many did not. "This poor behaviour disrupted learning in many classes and created an undisciplined atmosphere in corridors and public spaces," the report states.
The school struggled to combat bullying and both staff and parents agreed that it did not deal effectively with inappropriate behaviour.