Barrister Dinah Rose, president of Magdalen College, Oxford, defended students’ right to “free speech and political debate” as she urged people against issuing threats.
Her plea came after Education Secretary Gavin Williamson branded the move “simply absurd”.
Members of the Magdalen College Middle Common Room (MCR), which is made up of graduate students, overwhelmingly voted to remove the picture from their common room.
Political website Guido Fawkes reported that the motion was launched to make members “feel welcome”, with one student said to have commented “patriotism and colonialism are not really separable”.
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Ms Rose, who was appointed president of Magdalen College last year, tweeted: “So if you are one of the people currently sending obscene and threatening messages to the College staff, you might consider pausing, and asking yourself whether that is really the best way to show your respect for the Queen
“Or whether she’d be more likely to support the traditions of free debate and democratic decision-making that we are keeping alive at Magdalen.”
In a series of tweets, she emphasised that the students are not representative of the college, but added: “Magdalen strongly supports free speech and political debate, and the MCR’S right to autonomy.
“Maybe they’ll vote to put it up again, maybe they won’t. Meanwhile, the photo will be safely stored.”
Ms Rose concluded: “Being a student is about more than studying. It’s about exploring and debating ideas. It’s sometimes about provoking the older generation.
“Looks like that isn’t so hard to do these days.”
On Tuesday evening, Mr Williamson tweeted: “Oxford University students removing a picture of the Queen is simply absurd.
“She is the Head of State and a symbol of what is best about the UK. During her long reign she has worked tirelessly to promote British values of tolerance, inclusivity and respect around the world.”
Communities Secretary Robert Jenrick called the row “student union politics”, but he said he is “proud” to have a portrait of the Queen in his office.
He told BBC Breakfast on Wednesday: “I’m a huge fan and supporter of Her Majesty the Queen, I think we are incredibly lucky to live in a country with a head of state of her stature.
“I wouldn’t want anyone to disrespect her out of ignorance in this way, but I don’t think that we should waste too much time on student union politics.”