Some of the Royal Society's 1,450 fellows are unhappy at Duke of York's election and say 'royal fellows' should be phased out

After more than 350 years of largely happy association with assorted royalty, Britain's pre-eminent scientific institution, the Royal Society, faces unprecedented dissent from members after Prince Andrew was elected to become a fellow.

While the objections to the prince centre mainly on his slightly chequered career as a royal, a small number of the 1,450 or so Royal Society fellowship are asking the wider question of whether it is time for an institution based on science to end the practice of honouring people on the basis of heredity.

The controversy has been fuelled by the way the prince was elected to be a royal fellow, a status he shares with princes Philip, Charles and William, Princess Anne and the Duke of Kent, while the Queen is the organisation's patron. The ballots sent out to ordinary fellows provided only one box to tick, supporting the measure. Those opposed had to write "no" themselves or otherwise mark or spoil the paper.

The Royal Society, set up in 1660 with the encouragement of Charles II, announced Prince Andrew's election as a royal fellow on Friday, alongside the elevation of several dozen distinguished scientists and engineers to become scientific fellows, with the author Bill Bryson made an honorary fellow.

The dissent emerged later that day on the personal blog of David Colquhoun, professor of pharmacology at University College London and a Royal Society fellow since 1985. Colquhoun wrote that he was worried about controversies such as the 2007 deal which saw the son-in-law of Kazakhstan's president buy the prince's Surrey mansion for £3m more than its asking price, and the prince's friendship with Jeffrey Epstein, an American financier jailed for soliciting a minor for prostitution. The cumulative bad publicity saw the prince step down as a UK trade envoy in 2011.

Colquhoun told the Guardian that the prince, officially titled the Duke of York, was "an unsavoury character" who should not be associated with the Royal Society.

He said the organisation should consider getting rid of the royal fellow category altogether.

"I think it's an outdated concept. It was understandable that when the Royal Society was set up there was no democracy and no constitutional monarchy, you needed royal support, especially if you were doing something that seemed at the time a bit revolutionary. But it just doesn't seem to be appropriate in the 21st century.

"It's a category that really should be phased out now. The objects of the Royal Society are nothing to do with the monarchy, and the monarchy, on the whole, has shown absolutely no interest in science."

While scientific fellows have their credentials peer-reviewed by committees before being voted in at a meeting, by tradition royal fellows, as well as the organisation's president and vice-president, are chosen by a postal ballot giving only a "yes" box to tick.

Colquhoun made his own view plain by typing a message on to his returned ballot saying, in large, red letters: "I most certainly do NOT support the election of the Duke of York."

A total of 147 fellows voted for Prince Andrew in the postal ballot, with 24 returning spoiled papers, making for a turnout of 11%.

Another critic, Peter Lawrence, professor of molecular biology at Cambridge University, said he believed many more fellows had misgivings but played little active part in the society: "Every time I've talked to someone about this they look absolutely shocked. And I must say I share that. It shows up the anachronism of electing royal fellows.

"Having the monarch as patron is a nice tradition, but as for associated members of the royal family of uncertain relationship to science, I can't see the point. This particular election has probably highlighted this for many fellows."

He added: "I don't think this will reflect well on the Royal Society. My impression is that people will be highly critical of this."

A Royal Society spokesman noted that 85% of votes cast supported the prince's election. He said: "It's worth emphasising that it's a very small number of fellows who are making a lot of noise about this."

The prince was, the spokesman said, probably the royal who is most actively engaged with science, notably through a scheme to support young scientists and his work on links between science and industry.

He said: "Prince Andrew has been elected on the basis of what he's been doing to support British science and the Royal Society. Those who are not really involved in the day-to-day work of the society may not appreciate how closely he has been working with us on these issues."

The practice of not having a "no" box for royal fellow ballots was traditional, and was being looked at, the spokesman said. However, he added, fellows could easily voice dissent: "In this vote, and in previous ones, it's always made explicit to the fellowship how they register a no vote, whether writing 'no' on the ballot paper, or adding a comment, or whatever they choose."