Prince Charles' scientific prejudices were blamed this week for depriving leading scientists of honours.
The chief executive of the Medical Research Council, Colin Blakemore, was considering his future yesterday after indications that he had not been awarded a knighthood because he had been involved in animal research.
Colleagues of Professor Blakemore believe Prince Charles to be one of the key figures who blacklisted him for speaking out on the benefits of animal experiments.
The THES can reveal that academics at Oxford University boycotted the opening in February of a charitable research institute by Prince Charles because Professor Blakemore was instructed not to attend.
A senior academic, who asked not to be named, claimed: "The prince said he did not want to shake a vivisectionist's hand."
The Centre for Schizophrenia Research was funded by mental-health charity SANE, of which the prince is a patron. Academics assumed that Professor Blakemore would be presented to the prince because he was on the charity's board and had led efforts to raise money for the venture.
Academics and an MP said this week that Derek Burke, a former government adviser who criticised Prince Charles' views on genetically modified foods, had missed out on a knighthood for similar political reasons.
Professor Burke said: "There is a common perception that if you speak out against the prince, it is likely to be held against you. It looks to me as if the honours system is being used to suppress dissent, and that is damaging to democracy."
The palace declined to comment on the prince's views about animal research, but a spokesperson said: "Honours are drawn up and recommended by No 10 and finally approved by the Queen. Prince Charles has nothing to do with them."
Leaked minutes from the Whitehall committee that draws up the honours list, published in last week's Sunday Times , indicated that Professor Blakemore had been passed over for a knighthood because of fears of a backlash from the animal-rights lobby.
For years, Professor Blakemore has been one of a handful of scientists who have defended animal research publicly. He has suffered numerous threats from anti-vivisection extremists, including a bomb wrapped in needles addressed to his children.
Professor Blakemore told The THES that scientists who responded to the prime minister's encouragement to talk about research using animals knew they risked terrorist attacks. But "now we discover that, in private, the government considers such activity controversial and damaging to scientific reputation".
He said the news would delight animal-rights extremists but would have "a catastrophic effect" on the willingness of scientists to speak out on controversial issues.
He added: "Since the mission statement of the MRC includes engagement with the public about issues in medical research, this situation makes my position very difficult."
Outraged academics have been quick to support Professor Blakemore. Guy Goodwin, head of the psychiatry department at Oxford University, said: "We all owe him something for having put his head above the parapet. We should speak out against this."
Labour peer Lord Winston said: "The opinion that you should not give someone an honour because he has decided to speak up for what is government policy is revolting."
A senior academic said that he had seen an official document indicating that Professor Blakemore had been refused a knighthood on three other occasions.
Marjorie Wallace, chief executive of SANE, said: "I have supported nominations for him, and I can think of no other reason that he hasn't been chosen for a knighthood."
Labour MP Ian Gibson described the leak as proof that the establishment was "ganging up" on Professor Blakemore.