Oxford University's vice-chancellor says it is dishonest of politicians to link high levels of pay for university leaders with increases in tuition fees.
Louise Richardson accused "tawdry politicians" of undermining the UK's university sector.
She said that pay rates reflected a "global marketplace" and counterparts in the US were much better paid.
Universities minister Jo Johnson and Labour's Lord Adonis have warned against "excessive" pay levels.
"I think it's completely mendacious for politicians to suggest that vice-chancellors have used the £9,000 fees to enhance their own salaries," said Prof Richardson, speaking in London at the Times Higher Education World Academic Summit.
"We know that the £9,000 fees were a substitute for the withdrawal of government funding.
"My own salary is £350,000 - which is a very high salary compared to our academics - our junior academics especially, who are very lowly paid."
Value for money
But Prof Richardson said university heads' pay might not look so high compared with footballers or bankers.
She said that leading UK universities wanted to attract heads from around the world - and that meant competing financially in a "global marketplace".
In the United States, she said that more than 40 university leaders earned more than $1m (£770,000) and that some received more than $2m (£1.54m).
Universities have come under pressure over high levels of pay for senior staff - at a time when tuition fees and levels of student debt are increasing in England.
But Prof Richardson accused politicians of using this to undermine the higher education sector.
"I think this is just the politicians, and I wish they wouldn't do it, not because it's embarrassing for me or my colleagues but because it's damaging.
"Why would you want to try and damage what is one of the most successful aspects of the British economy?
"The calibre of university education is something that should be celebrated on a daily basis - not just trying to drag it down by making spurious correlations between fees and salaries."
Universities minister Jo Johnson has warned of the "upward spiral" in vice-chancellors' pay.
He told universities in July that they needed to do more to respond to students' concerns about value for money - "especially when some vice-chancellors take home a wage that in some cases exceeds that of the prime minister".
Labour's former education minister Lord Adonis has attacked the rising levels of pay for university leaders - at a time when students faced increases in fees and interest rates on loans.
Four MPs have resigned from their roles at the University of Bath, in protest at the pay received there by Prof Dame Glynis Breakwell, who is the highest-paid vice-chancellor in the country.
"At what point does it become justifiable to pay someone £450,000?" asked Bristol East MP, Kerry McCarthy, as she resigned.
Oxford head Prof Richardson also challenged universities to protect free speech on campus and to resist those who wanted to stop the airing of controversial views.
She said that students did not have a right not to be offended - and that universities had to be places where people might hear opinions they did not share.
"I've had many such conversations with students who come to me and say they don't feel comfortable because their professor has expressed views against homosexuality," said Prof Richardson.
"They don't feel comfortable being in class with someone with those views.
"And I say, 'I'm sorry, but my job is not to make you feel comfortable. Education is not about being comfortable. In fact, I'm interested in making you uncomfortable'.
"If you don't like his views, you challenge them, engage with them, and figure out how a smart person like that can have views like that.
"Figure out how you can persuade him to change his mind. It is difficult, but it is absolutely what we have to do if we believe in what we say, and I certainly do."