Last week, he ousted Sam Younger, the managing director of the World Service, in a classic move. It was presented as an amicable decision by Younger, and yet everyone knew he had been pushed aside by the BBC top brass. Maximum secrecy was in evidence, a replacement lined up, the corporate press managers were ready to spring into action with the approved spin.
The publication of Ariel, the staff magazine, was delayed for several hours until the deed was done, and another story, the appointment of Matthew Bannister as new head of BBC Production, was timed to draw away much of the attention.
Sir John is a man with an engineer's obsession for tidiness and order, and the World Service is not that sort of organisation; it is full of eccentric, extraordinary minds with a will of their own.
John Tusa, Sam Younger's high-profile predecessor at Bush House, regarded Birt with ill-concealed contempt, and when he was plain John Birt, Deputy Director-General, Tusa gave him a "hands off Bush House" warning that has never been forgotten or forgiven.
Sam Younger, through no fault of his own, is a victim of both the Birt- Tusa feud, and Birt's obsession with tidy structures.
In the aftermath of the shock restructuring of World Service, in June 1996, Younger was publicly assailed by Tusa, and many World Service staffers, for failing to resign on a matter of principle.
Younger had not been consulted about the changes, nor even told about them until the very last moment, and it is a widely held and plausible view that Birt banked on Younger falling on his sword, allowing him to be immediately replaced by someone more in the DG's own image.
A kindly and approachable manager, Younger stayed on and worked diligently to make the restructuring work, and managing to repair much of the damage done to relations with his staff. He demonstrated his modernising credentials by overseeing the recently announced rebranding of the World Service, and proposals for a news and current affairs channel, World Service Two.
If there were any criticism of him, it was that he needed to be tougher. And at the Corporate Centre, his attempts to convey the unique spirit of World Service fell on unsympathetic ears. We can, therefore, assume that this failure to demonstrate the required toughness, and to wholeheartedly embrace the Birt Philosophy, was ultimately his undoing. To survive as a Birt lieutenant, it is necessary to be, and to be seen to be, a true believer.
Younger's successor, Mark Byford, 40, is by all accounts, a talented broadcast manager - described by some as the acceptable face of Birtism - but challenging times lie ahead. He has arrived from his job as director of English regional broadcasting to discover that his ousted predecessor has already left his office and will not, as the BBC press release declared, "be leaving the BBC towards the end of the year". He also finds himself in the midst of a group of shocked and demoralised journalists and broadcasters from all points of the globe.
Among other things, Byford inherits an explosive issue: plans to reduce the number of foreign language services - there are currently 43 - to fund other aspects of the World Service operation.
To the majority of the 2,500 staff in Bush House, the BBC is not any old broadcaster. It is a shining light in a dark world, to be nurtured and loved. They cannot understand why something that even Lady Thatcher admired as a national asset should be so relentless hammered from within.
No sensible person would deny that, in the days when the BBC World Service was known as External Services, it was a complacent, often arrogant, organisation.
It, and the rest of the BBC, probably needed Birt, or a Birt-like figure, to rattle the cages - but five years of this would have been more than enough.
Ian Richardson is a former senior journalist and manager with BBC World Service radio and television. He now runs Richardson Media, writing and lecturing on media-related issues