Mark Damazer, previously controller of Radio 4, became master of St Peter's College in October. He said both Oxford and the BBC had sometimes struggled in the face of a "determinedly hostile" media, but should remain committed to their "noble" aims.
At the recent annual conference of the Higher Education Academy in Nottingham, Mr Damazer said the furore over Laura Spence, the straight-A state-school pupil turned down for a place at Oxford in 2000, was an example of unfair criticism.
"At its crudest, the critique implies that Oxford picks those with the right accent or face or connections," he said. "When inaccurate statements are made - even if they are genuine mistakes - it may make it harder to convince those who might apply, and might get in, to do so.
"The admissions system is vastly, and rightly, more professional than in my youth. It is an attempt at meritocracy - imperfect...but a very real one."
He said many of the attacks on his former employer were also "baffling" and part of a "BBC criticism industry. The torrent of negative publicity can have a painful and distorting effect," he admitted.
But Mr Damazer said that academics should not be put off by accusations of elitism. "The BBC and Oxford are elite organisations", he said, "by which I mean that they stand for excellence and strive hard - in an environment often determinedly hostile - to sustain their purposes which are noble and worth defending - imperfections and all."
He also defended Oxford's one-to-one tuition system, calling it "magical in its conception and impact".
Mr Damazer's comments came as data released by the Office for Fair Access revealed that Oxford planned to spend more of the extra income from higher tuition fees on widening access than almost any other university in England.
It has pledged to spend 51 per cent of the additional income from fees over £6,000 on such activities, compared with the University of Cambridge's 32 per cent.