Last week this master of thorough preparation came unstuck - in the process plunging his new boss into another internal crisis. In front of a committee of MPs, Sir John defended the job done by his officials over Sierra Leone, thereby contradicting accounts given by ministers. Within hours, the head of the diplomatic service had retracted his evidence in what one newspaper labelled a "Whitehall farce".
The episode added little to public understanding of the arms-to-Africa affair, but underlined the inability of ministers and officials at the Foreign Office to act and speak as one. With accusations that diplomats were running policy without informing ministers, and counterclaims that Mr Cook and his Minister of State, Tony Lloyd, were incompetent or lazy, the grandest department in government was back in ferment.
This is hardly the first example of tension between a Labour Foreign Secretary and his civil servants. George Brown enjoyed an uneasy relationship with officials, and David [now Lord] Owen, arriving from Health and Social Security, was shocked by the attitude of officials. At the DHSS, he wrote, "they were much more relaxed about the idea that one minister made the decisions", while "some of the Foreign Office found it immensely difficult to accept that diplomacy could be subject to the same degree of ministerial authority. They thought diplomacy was a different thing from everyday authority, and that special skills were required for it, which they had and the secretary of State did not." Little surprise that Tessa Blackstone, now an education minister, then a member of James Callaghan's Central Policy Review Staff, was dispatched to propose reform.
With Conservative grandees such as Lord Carrington, Sir Geoffrey Howe or Douglas Hurd at the helm, internal workings were smoother. But Number 10 was not so happy, believing the Foreign Office to be an institution susceptible to all things European and temperamentally committed to negotiation and compromise rather than defending the national interest to the death. According to one senior Tory, the diplomatic service was made up of "effeminate first secretaries floating around the Paris cocktail parties, but no one selling tractors in Lille".
Tension is back with a vengeance. A clash of cultures is hardly surprising given Foreign Office traditions and the radical roots of its current boss. Despite reforms, the diplomatic service remains an elite institution, both academically and socially. Of last year's recruits to the all-graduate fast-stream, 48 per cent were from Oxford and Cambridge and 60 per cent from independent schools. Just 1.1 per cent of the diplomatic service comes from an ethnic minority.
The Foreign Office is the most palatial of the Whitehall buildings and the Foreign Secretary's office is large enough, according to one former occupant, to accommodate three double-decker buses. Visitors cannot escape reminders of Britain's past in Europe and beyond; receptions are held in the Locarno rooms or the Durbar Court. Nor is this sense of style and history restricted to London. One ex-minister harks back to an overnight stay in the British embassy in Paris: "There were footmen, there was a four-poster bed, fresh orange juice and croissants in the morning and a copy of the Times specially flown out."
Little wonder that when the BBC proposed to film a documentary on the Foreign Office in the last parliament, the diplomatic top brass were in two minds about the idea. "The trouble," confided one mandarin at the time, "is that all the good, positive exposure of our work on the ground is destroyed by one shot of an embassy cocktail party."
BUT this is only part of the picture. One of the paradoxes of the Sierra Leone saga is that two of the officials embroiled are regarded as proponents or symbols of change. Sir John's modernising attitude is contrasted by Mr Cook's allies with that of his predecessor, who, "for a long time couldn't understand what we wanted to do and when he did, didn't like it". When Mr Cook appointed an ethnic minorities liaison officer to help recruitment, Sir John appeared at an internal meeting to speak up for the initiative. Ann Grant, head of the Africa department, which is at the heart of the row, is a graduate of Sussex (ie not Oxbridge) and spent a chunk of her career at Oxfam.
Through the 1990s the Foreign Office has re-oriented itself away from narrow diplomacy towards the demands of business, stepping up collaboration with the Department of Trade and Industry. Small European consulates were closed in favour of emerging areas in the east (although the diplomatic presence is small compared to other nations). Even the Paris embassy, under Sir Michael Jay, has tried to present a forward-looking image, decorating its walls with some modern art works which anticipated "Cool Britannia".
But Mr Cook wants to up the pace of these changes. He has already held one open day at the Foreign Office, and plans another for recruitment in June. Ethnic-minority groups at universities have been targeted. Already there are signs of success; of those applying for this year's mainstream, 25 per cent are from ethnic minorities, and Keith Vaz, MP for Leicester East, has praised the efforts as an example to Whitehall.
There are other threats to the old order. Earlier this year, Cook founded an independent institute to generate foreign-policy ideas, the Foreign Policy Centre, seen by some as a direct challenge to those traditionalists who believe in the Civil Service dominating advice to ministers. Many Labour figures believe there is much more to be done. George Lawson, a researcher at Demos, the New Labour think-tank, argues: "The Foreign Office is one of the bastions that thinks it has to keep information secret. They are still living yesterday's politics and do not understand that information is held too widely for most of it to be kept secret indefinitely."
This agenda, allied to Mr Cook's occasionally brusque style, has put backs up. The minister has also offered some hostages to fortune. His promise of a foreign policy with an ethical dimension has opened up the department's activities to particular scrutiny. His insistence on the need to concentrate on the big picture, rather than consuming briefing papers, has led to charges of arrogance.
OVERWHELMED by the demands of the European presidency and a series of international conferences and commitments, Mr Cook has scaled down meetings with the mandarins. Diplomats are clever people who expect their advice to be taken, and this has not gone down well. One source admitted: "There may be people who feel that when the ambassador of Woggadoo is back in London he should see Cook. That doesn't happen - but it probably wouldn't with any foreign secretary during the presidency."
This mixture of personal and ideological differences has explosive potential, as Mr Cook's political stock falls. As one veteran civil servant put it: "If you give the impression you're not happy with your department, you're not doing all your paperwork or you think you can get by on your intelligence, you are asking to be taken to the cleaners."
But the mandarins of the Foreign Office may be exposed, too. Mr Cook has promised an internal review of the Sierra Leone affair and his friends say it may be used to speed up the pace of change. Perhaps that is why Sir John's slip-up was being seen at King Charles Street as unqualified bad news - for everybody.
Ten facts about the Foreign Office
The Foreign Office budget is pounds 1,008m.
It employs 5,850 people.
Britain has diplomatic relations with 186 countries.
There are 145 high commissions and embassies.
The Foreign Office owns 3,900 properties.
Land and property overseas is worth pounds 937m.
34 per cent of overseas staff promote British exports.
There were no senior ethnic minority staff in 1997.
The highest-paid mandarin earned around pounds 115,000 in 1997.
The Foreign Office owns 850 cars and 280 vans and lorries.Reuse content