Speaking on Radio 4's Saturday Live programme yesterday, Paxman, who is rumoured to be in the running to become the new director general of the BBC, said: "The thing I like about British identity is that increasingly, since there's such a head of steam building in ... Scotland for hating the English, I find myself describing myself as English when in fact I'm a quarter Scottish."
The comment by the Newsnight host, whose grandmother was from Glasgow, comes amid criticism of the BBC over alleged bias in its reporting of the independence debate.
Several hundred people are expected to attend a protest at the BBC's Glasgow HQ at Pacific Quay today over the broadcaster's alleged anti-Yes coverage of the referendum
Professor John Robertson, of the School of Creative & Cultural Industries at the University of the West of Scotland, has produced a new report examing a perceived institutional anti-independence bias in BBC news reports. Robertson has criticised BBC coverage previously, and been rebutted.
Paxman was speaking about the notion of "Britishness" on BBC Radio 4 when he revealed he was fascinated by Scotland and would one day like to write a book on the country's contribution to the British Empire.
He added: "What is British identity? It is what it is. The thing I like about British identity is that increasingly, since there's such a head of steam building in ... Scotland for hating the English, I find myself describing myself as English when in fact I'm a quarter Scottish.
"The thing I like about Britishness is that it is inclusive. You can be Belizian British, Asian-British, English British, Scottish British ... Northern Irish British, even. Britain was essentially an invention to do with the growth of empire and religion.
"There were many things that made up Britain and empire was one of them."
Commenting on the referendum vote, he said: "It's interesting, isn't it, that in this union of supposed equals only one side gets to vote on whether the union should continue or not." He then added cryptically: "If I was north of the Border I would vote opposite to the way I would if I was south of the Border."
Paxman later modified his comments about hatred of the English when questioned by the show's presenter Aasmah Mir, saying: "Hate is too overstated and I expect I overstated it, and I do apologise. But it is to do with a detestation of being ruled from London."
His comments echo those made by his BBC colleague Andrew Marr while speaking at the Edinburgh International Book Festival last August. Marr claimed Scots' hatred of the English can be toxic, saying: "There is very strong anti-English feeling and everybody knows it, there always has been. If you go back to the origins of the SNP and the origins of the debate about home rule, anglophobia was as well entrenched then as it is now. It can become serious, it can become toxic."
A spokesman for Yes Scotland said he would be interested to read any book on Scotland by Paxman, adding: "He would realise very quickly, with only limited research, that he is mistaken in his assertions.
"We are fortunate to have a good number of lead volunteers who are from England. They demonstrate the fact that the case for independence is made in many accents.
"The case for independence is about democracy, not identity. We are finding that the opportunities for the economy of the north of England - with a more successful Scotland providing a counterbalance to London - is of particular interest to English people in Scotland."
He added: "The 'Go for it Scotland' campaign is another part of our approach with leading figures in England and across the UK making clear their support for Yes."
The issue of alleged anti-independence bias at the BBC is becoming increasingly central to the debate, with some Yes campaigners concerned at the influence the state broadcaster wields with its news reports.
Earlier this year, Robertson produced a report on the "fairness" of BBC reports to either Yes Scotland or Better Together, and concluded that the majority of reports were negative towards independence.
He has now carried out a second survey of a month of editions of the flagship BBC Radio Scotland programme Good Morning Scotland, and found that, in his opinion, it also displayed a similar level of bias.
His report said: "These broadcasts were balanced, in crude numerical terms, but in every other respect, unfair to the Yes campaign and favouring the Better Together campaign."
He found that news segments often began with bad news for Yes and featured heavy repetition of such messages over several hours. Statements from the Yes perspective were often reactive while those favouring Better Together given prominence.
Interviewers also tended to adopt aggressive techniques with Yes supporters while only doing so on two occasions with BT supporters.
He said: "The BBC clearly needs a system of monitoring and balancing of its content to limit the admittedly unavoidable intrusion of bias to a minimum. It is wrong that research of the kind reported here and earlier, regarding TV news, is required in a democracy."
A spokesman for BBC Scotland denied there was a bias towards a No vote, saying: "We reject claims of bias in our reporting of the referendum in our output, including Good Morning Scotland. Our coverage of this major story continues to be covered according to our editorial guidelines on fairness and balance."