Sir Robert May announced that there was "not much of a case" for the ban and claimed that it was politics rather than hard evidence that had persuaded ministers to keep it in place.
Sir Robert's comments contradicted the Minister of Agriculture, Nick Brown, who decided to extend the ban by six months on the grounds of scientific advice and because the need to protect public health was "paramount".
Mr Brown infuriated farmers but claimed that he had to follow the advice, revealed in The Independent, of the Chief Medical Officer, Liam Donaldson, that there was still a small risk of BSE remaining in beef bones.
But Sir Robert, the Department of Trade and Industry's most senior scientist, said that the ban was "a mixture, in my view, of a political and scientific decision. On purely scientific grounds I personally don't see much point in banning beef-on-the-bone," he told BBC radio.
"But you have to see it in a much wider context of the past history, particularly in Europe," he added.
The Shadow trade and industry secretary, John Redwood, said that Sir Robert's comments proved the "humbug" of the Government's stance.
The National Farmers' Union also welcomed his comments, claiming that they proved the six-month ban should be lifted immediately.
"We have always said that, based on the scientific evidence available and the minute risk from beef-on-the-bone, consumers should have the freedom to choose whether they eat it or not," a spokesman said.
"Whether the decision is scientific or political, the fact is that the ban has not been lifted yet. In term of our members this may cause concern but to a certain extent it doesn't matter what the reason is."
A leading Blairite think-tank claimed last night that the beef-on-the- bone ban may have been motivated as much by the demands of Europe after the BSE-crisis as by concern for human health.
Demos said that it was time for the Government to stop using "pseudo science" and allow consumers to make up their own mind about beef on the bone and genetically modified foods.