The ancient and mysterious institution of crown appointed professors is under attack.

It was a cold mid-January morning when the letter from Downing Street arrived at the porter's lodge of Christ's College in Cambridge. Quentin Skinner, a professor of political science, who was busily preparing for a lecture tour to Yale and Princeton, opened the envelope and read the contents of the surprise prime ministerial epistle. Before long, he was sitting in Number 10 and accepting the star post in the academic historian's firmament - the regius chair of modern history. His appointment ended months of senior common room speculation and marked the moment when Downing Street could once more shroud in mystery the most secretive appointments machinery in the modern university world.

Skinner was hotly tipped to succeed the current regius professor Patrick Collinson, who retires in September. A brilliant undergraduate - he was elected straight into a college fellowship at the age of 21 after taking a virtually unheard of double starred first - Skinner, now aged 55, has established himself as Cambridge's classiest historian and a world authority on Machiavelli and Renaissance republicanism. The great 18th-century scholar J. H. Plumb, who taught him in the early 1960s, talks of "the miracle of Quentin", and Collinson regards him as the "obvious successor".

But, even with such impeccable testimony, there could be no guarantee that Skinner would get the nod of approval. That is because the regius professorship, as its name suggests, is a crown appointment. Officially, the Queen chooses, but in practice the prime minister, exercising the royal prerogative, makes the final choice, aided by a shadowy Trollopian "patronage secretary". There is no advertisement, no interview even, just a constant round of closet consultations and surreptitious "soundings".

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In the case of Skinner, the patronage secretary - John Holroyd, a senior civil servant who rarely strays far from Downing Street's inner sanctum - visited Cambridge last October. Over two days, he listened to everyone from the highest professor to the lowest university lecturer, and he would have learned that Skinner was the history faculty's favoured candidate. Yet, right to the last, the result was in doubt, and rumour rampaged through Cambridge that the politicians had overturned the wishes of the academics. Two days before the announcement, a leading faculty member was "reliably informed" that an American-based historian was "negotiating terms".

In the end, however, Cambridge got its man. But the last minute flutter - real or imagined - has been enough to set some dons talking of reform, if not outright revolution. At an official level, Cambridge and Oxford, which is about to undergo the same process to find a successor to Renaissance historian Sir John Elliott, are reticent about revealing plans to reform the system. Oxford is content simply to issue a formal statement which grandly cites the "royal prerogative" to explain its vice chancellor's blunt refusal "to discuss the matter or to make any comment" - somewhat surprising given that Lord Jenkins of Hillhead, the university's chancellor, has been particularly outspoken on the question of open government since the publication of the Scott report. Cambridge is only marginally less guarded, with vice chancellor Sir David Williams acknowledging fuzzily that the appointment process of all professorships has been examined "for some years". But, for all the obfuscation, it is clear that the spotlight has been turned on crown appointments and what one regius professor calls, with casual familiarity, "the review". Downing Street admits as much, referring to "continuing discussions". It could lead to the transformation of a royal system of appointments which has survived nearly 500 years.

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The first regius chairs were established in Scotland. The oldest, Aberdeen's regius professorship of medicine, dates back to 1497. Most of the Oxbridge regius chairs - there are eight at Oxford and seven at Cambridge - were founded by Henry VIII in the 1540s, although the history chairs did not appear until 1724. The system of crown appointments received further endorsement this century, first with the setting up of Cambridge's King Edward VII professorship of English in 1912 and then with the foundation of Churchill College in the 1950s where the master, as at Trinity in Cambridge and Christ Church in Oxford, is chosen by the prime minister.

Some of the regius chairs still carry the mark of medieval midwifery. Sir David Weatherall, Oxford's medicine professor, has to serve as the master of the alms houses of Ewlme, a task supposedly set for his predecessors by Chaucer's great grand-daughter. In the absence of any special perquisites - the regius professor is paid the same as other professors - it is this, the link with the ancient past, which gives the regius professorship its peculiar status and makes it very difficult to turn down. More than 100 years ago, Macaulay rejected the regius chair, commenting that "it would be strange if, having sacrificed for liberty a seat in the cabinet and Pounds 2,500 a year, I should now sacrifice liberty for a chair at Cambridge and Pounds 400 a year". But the recent trend has been to take the title. At the height of the cash-grabbing 1980s, Collinson took a Pounds 3,000 pay cut when he left his Sheffield professorship while Elliott waived a handsome reward from Princeton.

In little old England, tradition still talks. Yet the call for change is getting louder. Collinson - who describes himself as "old-fashioned, slightly left of centre, vaguely progressive, liberal" - says the appointments system is "anomalous" and suggests there is a feeling in Cambridge "that one should catch up with the 20th century before it ends". Jonathan Steinberg, vice-master of Trinity Hall and chairman of Cambridge's history faculty, speaks plainly of the need to "depoliticise the process".

It is indeed a supreme irony that John Major, a man of negligible academic achievement, has already appointed seven of the 12 Oxbridge regius professorships which fall within what John Colville, Winston Churchill's patronage secretary, once called "the Downing Street demesne". He has also been involved in the selection of two of the three crown-appointed Oxbridge masters - the Very Reverend John Drury, dean of Christ Church in Oxford, and Sir John Boyd, the ambassador to Japan who takes up the Churchill College post in October.

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Weatherall suggests that he has never, during John Major's administration, "sniffed any hint of political interference". But, in the past, prime ministers have wielded considerable influence. There is the famous case when Harold Macmillan selected the conservative Hugh Trevor-Roper instead of the radical A. J. P. Taylor to fill the Oxford chair in the 1950s. More recently, Margaret Thatcher installed the military historian Michael Howard in 1980, causing an outcry among those Oxonians who thought that left-leaning Keith Thomas should have been appointed. Oxford professor Norman Stone, who walked in Thatcherite circles in the 1980s, says that Mrs Thatcher might have exercised some influence, "especially given that she was dealing with the disarmament issue at the time".

The no-turning-back prime minister eventually U-turned on the practice of forcing her political will on professorial appointments. "She realised," says Stone, "that to go against the consensus would cause a lot of fuss - and for what?" The sea-change serves to demonstrate that the personal preference of the prime minister is paramount, and this fact was brought home to Collinson in 1987. Mrs Thatcher had written "a big fat letter" to him, offering the Cambridge chair. He did the decent thing, thought about it for a couple of days, and then accepted. But before the appointment could be given the royal seal of approval, the general election was called. It remained a very real possibility that an incoming Labour government could veto Thatcher's appointment. "My dream scenario," remembers Collinson, "was for Kinnock to win, confirm my appointment, and then I would have had two letters from two prime ministers which I could have had framed and put on the wall in my loo."

If reform is on the horizon, it seems unlikely that the right of prime ministers to choose the three Oxbridge masterships will be revoked. At Trinity, according to senior tutor Graham Chinner, "there are no republican rumblings". Back in the 1960s, Harold Wilson appointed the Conservative minister Rab Butler, in part to remove him from the opposition benches. The Trinity fellows were horrified because Butler was not "a Trinity man". But in the end, it turned out rather well, and Butler stayed on for an extra five years. Across at Churchill, where a non-scientist has just been appointed for the first time in its short history, the fellows are equally happy with the status quo. Mark Goldie, the vice- master, says "there is no active move to change the system", although he expresses a personal preference for change because "institutions should be allowed to be autonomous".

But the chance of changing the system for appointing regius professorships is high because some regius chairs are already outside the political fray. In Cambridge, three - divinity, Hebrew and Greek - have never been chosen by the prime minister. Instead, a board of electors makes the selection, like any other professorship. In Scotland, where three universities - Aberdeen, Glasgow and Edinburgh - boast an unmatched total of 35 regius professorships, a selection board makes a recommendation to the secretary of state for Scotland.

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If they were feeling radical, Oxford and Cambridge could lobby for the remaining 12 crown-appointed professorships to be decided in the same way. The more likely option, however, is the adoption of a procedure introduced during Callaghan's premiership for the appointment of bishops. Goldie calls this "the middle way", and it limits the prime minister's choice to two names submitted by the university. This has several advantages. It is a familiar system for the patronage secretary, who advises on the selection of bishops and who is known in ecclesiastical circles as "heaven's talent scout". It also recognises what many academics think is one of the merits of the crown appointments system: the wide, one don even calls it "democratic", consultative process. Most professors are elected by their peers, and the competition is often ruined by faculty faction fighting. "You often end up with a compromise candidate," says Stone. By contrast, the crown appointment rises above the fracas of faculty frictions, and more than 50 academics outside Cambridge were consulted on the Skinner appointment.

It makes sense. But John Major, the most famous alumnus of the university of life, evidently likes the privilege of choosing the finest brains in Britain. Only last year, he instructed Holroyd to tell a delegation of Oxbridge dons that he "must exercise the royal prerogative in a real sense and not as a mere formality". On the other hand, the Labour party has said that it is prepared to introduce "procedures in tune with the 21st century rather than Trollope and the 19th century". So perhaps the days when the prime minister's envoy arrives at the gates of the ancient universities in magisterial fashion - "surrounded by the canopies of state and supposing that supplicant dons will go down on their hands and knees offering frankincense and myrrh", as one observer puts it - are truly numbered.

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