Outspoken neuroscientist and animal activist target Professor Colin Blakemore, 70, has said he is "delighted and surprised" to be knighted after controversially being overlooked by the honours system.

Sir Colin, who is included in the Queen's Birthday Honours List, is the only former chief executive of the Medical Research Council (MRC) to have left the post without a knighthood.

Leaked government documents suggesting he had been snubbed due to his high-profile association with animal research led to his threatened resignation as head of the MRC in 2003.

But putting the political controversy behind him today he said: " Life has its ups and downs: this is definitely an up!"

Sir Colin, currently director of the Centre for the Study of the Senses at the University of London's School of Advanced Study, added: "This is the cream on the cake - final evidence that things have changed right to the top of society.

"Obviously I'm delighted. I can't imagine anyone who is included in the honours list not being overwhelmed and pleased about it.

"In many ways I'm surprised, not least because of the events of 10 years ago.

"Attitudes have changed enormously over the years and the sort of stance I and others took is now much more recognised and seen much more positively. But it was still difficult to believe that opinions could reverse in this way."

He insisted that when he threatened to resign it was not out of "pique" but because his work was threatened.

"It's very easy to misinterpret what I did," he said. "I just found myself in an untenable position because I was pursuing a policy of activism and communication in the MRC, appealing to scientists to involve themselves in public debate. I just felt my effectiveness was really being undermined.

"It became clear that people who were willing to get involved in controversial issues could be persecuted in secret. I found that disturbing but it wasn't personal pique.

"I feel very seriously that public honours should not be used simply to reward someone for their job."

Documents leaked to The Sunday Times in 2003 indicated that Sir Colin had deliberately been excluded from the forthcoming New Year's Honours List.

Normally it is automatic for an MRC CEO to be knighted.

Sir Colin told the British Medical Journal later: "It is paradoxical when you engage in robust dialogue and at the same time the honours process suggests that by doing so you damage your reputation and are too controversial. It is outrageous."

He only withdrew his resignation threat after a parliamentary inquiry and the intervention of then prime minister Tony Blair and the government's chief scientific adviser, Sir David King.

Sir Colin continued running the MRC until 2007, but still a knighthood eluded him.

In the 1980s and 1990s, his open support for animal testing made him the target of a terror campaign. One experiment in particular that involved sewing down the eyelids of kittens to study the development of vision in the brain enraged animal activists.

While many of his peers cowered before intimidation and threats of violence, Sir Colin continued to justify his work to journalists, politicians and anyone who would listen.

As a result, he endured regular loud abusive protests outside his house, smashed windows, letters laced with razor blades, parcel bombs, kidnap threats directed at his children, and physical assaults.

"It was tough in those days," he said. "I was really in the eye of the storm. But giving in would only have made that kind of campaign more effective. That's what they wanted, to silence me.

"Now the really violent extremists have been locked up and the whole tenor of the debate has changed completely. The kind of violence I suffered just doesn't happen at all. Public attitudes have changed as well."

Throughout his academic career at the universities of Cambridge, Oxford, Warwick and London, Sir Colin has championed the communication of science to a wider audience.

In 1976, aged 32, he became the youngest person ever to deliver the BBC Reith Lectures - a series of six talks entitled "Mechanics of the Mind".

He has subsequently presented or contributed to hundreds of radio and television broadcasts.

Since 2004 he has been honorary president of the Association of British Science Writers.

Professor David Nutt, head of the Department of Neuropsychopharmacology and Molecular Imaging at Imperial College London - himself no stranger to controversy - said: "From inspirational junior lecturer in Cambridge University, through Prof of Physiology at Oxford to restructuring the MRC as CEO, Colin has shown a unique ability to combine scientific rigour with innovation and intellectual honesty. The UK scientific community will welcome this long-overdue recognition."

In 2009, Prof Nutt was dismissed from his former job as the Government's chief drug adviser after claiming that ecstasy and LSD were less dangerous than alcohol.

Professor Simon Wessely, president elect of the Royal College of Psychiatrists and vice dean at the Institute of Psychiatry, King's College London, said: "Most of us can remember very little of who taught us back when we were medical students in the dim and distant past. But there was one lecturer who filled the Cambridge lecture hall, even on the Saturday morning slot that he was given.

"So 40 years ago (although I am sure he will not thank me for saying that), Colin was the maestro of not just neuroscience, but also of science communication. This is a fitting tribute."

Fellow neuroscientist Professor Richard Morris, from the University of Edinburgh, said: "I am delighted to learn that Colin Blakemore's many contributions to science, to the public communication of science, and to charitable causes related to medicine have now been recognised by the country he loves.

"He has been a tireless campaigner for an evidence-based approach to all of these causes. Biomedical science in the United Kingdom owes much to him, even now as he continues with new research on brain and mind."

Professor Sir John Savill, chief executive of the Medical Research Council, said: " I am delighted that Professor Colin Blakemore, former chief executive of the MRC, has been awarded a knighthood.

"Professor Blakemore is a highly regarded researcher and has served UK science over many years extremely well in a large number of ways. His support for the use of animals in research has been extraordinarily brave; he led the way on openness at a time when this was at great personal risk to himself and his family."

Dr Jeremy Farrar, director of the Wellcome Trust, said: "I am absolutely delighted to hear that Colin's enormous contribution to science and society have been recognised with such an honour. This is fully deserved by someone who has challenged, stimulated and inspired in equal measure and always with a wonderful sense of humour.

"Besides his ground-breaking work in neuroscience, he has paved the way for open communication on scientific issues of public importance. He was one of the first to speak out honestly and bravely about the use of animals in research and the new concordat on openness is very much a part of his legacy.

"Colin has helped create a thriving environment for science and medical research in the UK of which we can all be extremely proud, and, on a personal note, I have been enormously grateful for his wise council and sage advice."

Tracey Brown, director of the organisation Sense About Science, said: "This is recognition of something that some of us have known for a long time, that Colin Blakemore is not only an excellent scientist but a genuine leader in discussing the most difficult research issues openly with the public.

"He has had to cope with more challenges than most, including threats to his personal safety, and amongst it all he has been braver than most. He put himself forward for public discussion on the hard issues, from animal testing to the MMR vaccine controversy, at a time when the authorities ran for the hills."

Wendy Jarrett, chief executive of Understanding Animal Research, said: "I am delighted to hear that Colin Blakemore has been honoured in this way. His achievements speak for themselves, but they are all the more remarkable when one considers that for many years he pursued his ground-breaking research under concerted attack from animal rights activists.

"The fact that he did not give in to their violence and threats, and indeed made a point of talking openly about the importance of animal research in medical progress, is testament of his strength of character. He has encouraged many more scientists to speak up about their research using animals, helping the public to understand why such research remains necessary in some circumstances."