The veteran DJ has pledged to take legal action against the corporation, which he claims is making him a "scapegoat" for the "cover-up" of abuse of an under-age girl.
His shock departure comes ahead of the publication on Thursday of a report into the BBC's culture and practices during the years Jimmy Savile and fellow shamed presenter Stuart Hall worked at the corporation by former Court of Appeal judge Dame Janet Smith.
Blackburn, 73, claims that "all relationships" he had with the BBC were "terminated with immediate effect" this week because his evidence to the review over an investigation in 1971 contradicts the BBC's version of events in relation to an allegation of assault by the mother of a 15-year-old who later committed suicide.
He says he was never interviewed over the incident but claims the BBC says he was interviewed twice, reports Press Association.
In a statement he said: "Sadly what is happening to me now seems to be entirely in keeping with the past BBC culture of whitewash and cover-up.
"Naturally, I am now left with no choice but to take legal action against the BBC. They have taken away a career I love and I will not allow them to destroy my reputation."
Listings for Blackburn's two upcoming BBC Radio London shows on the BBC website say that fellow DJs Jaki Graham and Lemar will be sitting in for him.
Information for his scheduled Radio 2 vintage chart Pick Of The Pops still states he will be presenting.
The BBC declined to comment.
Blackburn's full statement reads: "This week, two days before the publication of the Dame Janet Smith Report , the BBC informed me that all relationships I had with them were being terminated with immediate effect.
"I am told that the decision was taken, personally, by the Director General. Quite naturally, I am devastated.
"The reasons for the BBC taking this decision are that my evidence to Dame Janet Smith shows, I believe, that a cover up took place - one that I had no knowledge of.
"This goes against what the BBC believe.
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"In 1971 allegations were made by the mother of a 15 year old girl whose diary apparently contained suggestions that she had been seduced by celebrities including me.
"I am told that the mother told the BBC, a few weeks after her initial complaint, that her daughter had withdrawn the allegation against me.
"I have never seen the diary and neither has anyone at the BBC or the Dame Janet Review.
"That same year this seemingly troubled teenager, tragically took her own life.
"Dame Janet’s report makes no suggestion that I was guilty 45 years ago of any misconduct whatsoever with this girl.
"Nor did a Coroner’s inquest into her death or a subsequent police inquiry. The BBC have made clear that they are not terminating my relationship with them because of any misconduct.
"They are destroying my career and reputation because my version of events does not tally with theirs.
"I was not guilty of any inappropriate conduct; my lawyers will take immediate action against anyone suggesting that I was.
"According to BBC records seen by Dame Janet, I was allegedly interviewed about the girls’ diary before her death in 1971 by a very senior figure at the BBC, Bill Cotton Jr.
"I was also, supposedly, interviewed by Brian Neill QC as part of his report in to the Payola scandal at the BBC.
"I have repeatedly told Dame Janet and the BBC I was never interviewed by either man in this context and the BBC records are either very vague or have, conveniently, disappeared.
"Regardless of these facts, the BBC is axing me after five decades of broadcasting.
"Sadly what is happening to me now seems to be entirely in keeping with the past BBC culture of whitewash and cover-up.
"In 1967, I proudly opened Radio 1 for the BBC.
"Over the past 49 years I have enjoyed my time working for them immensely and I am grateful to my millions of listeners for their continued support over the decades.
"Sadly, despite being aware of my evidence for many months, if not years, the BBC have decided to make me a scapegoat and have taken away any future opportunity I have to broadcast for them.
"Naturally, I am now left with no choice but to take legal action against the BBC.
"They have taken away a career I love and I will not allow them to destroy my reputation."