The special advisor Jo Moore's close relationship with Stephen Byers made it impossible for civil servants to discipline her when internal conflict ripped apart her department, a highly critical report by a committee of MPs will conclude this week.
Failures in Whitehall's management system created an irreversible breakdown in the relations between Ms Moore and the department's press office and led to a series of damaging leaks to the press.
A report by the Public Administration Select Committee will say that Ms Moore's unique status in the department and her close political ties to the former secretary of state for transport led to resentment among his press officers who complained of bullying and lack of control.
The spin doctor's personal appointment by Mr Byers and her status as "a political animal" gave her special protection that other civil servants did not enjoy.
The MPs will paint a picture of a dysfunctional Department of Transport, Environment and the Regions under Mr Byers where the government press officers were in effect at war with Ms Moore. It will say that resentment led to a series of damaging leaks of highly sensitive information, including the e-mail in which she said 11 September was a good day to bury bad new.
The report will say that managers, including the Permanent Secretary, Sir Richard Mottram, did not have enough guidance on conflict resolution to cope with the crisis.
The examination of the events that led to the departures of Ms Moore, of Martin Sixsmith, the communications director, and ultimately the secretary of state, does not lay all the blame for the breakdown with individuals including Mr Byers. The report concludes that Mr Byers was also failed by the breakdown of the system and the unprecedented chain of events.
But normal procedures for disciplining Ms Moore, after the e-mail leak, failed because the civil service felt nobody but Mr Byers could sack her.
The report, called These Unfortunate Events, said the codes of conduct and Whitehall "system" were incapable of dealing with the unprecedented dispute that broke out.
The MPs say that Sir Richard felt his hands were tied when it came to firing Ms Moore. "Mottram did not want to poison the well with the secretary of state. There was a weak response," one source close to the committee said. "It all went wrong because the people involved were at the top of the department."
The report does not single out Ms Moore or Mr Sixsmith for attack but does condemn the flow of leaks from Whitehall, which helped destabilise the department.
"The theme is that the system is inadequate to deal with the situation that arises when a special adviser is breaking the rules and that special adviser has a close relationship with the secretary of state," said one source who has read the report.