Theresa May faces a showdown with the Queen – over scrapping ¬seven of Her Majesty’s royal charters.
The royal charters guarantee that scientists are independent of the Government and can carry out whatever research they choose.
They are now concerned they will lose that freedom and might be subjected to political interference.
Constitutional expert David Rogers said: “The Queen will hit the roof and it will cause a huge dust-up with the PM.
“This could turn into Mrs May’s first row with Her Majesty since she became PM. The Queen is likely to raise it with Mrs May at one of their weekly audiences before she signs it into law.”
The huge change is being overseen by Universities minister Jo Johnson, brother of Foreign Secretary Boris.
He plans a major shake-up of higher education in a Bill now going through Parliament.
Under his plans the seven bodies – including the Medical Research Council, Economic and Social Research Council and the Natural Environment Research Council – will be amalgamated as UK Research and Innovation.
The new body will not have a royal charter.
Critics also say that the 50 universities governed by royal charters will have them overridden by the new Office for Students.
That would allow ¬ministers to tell universities what courses to teach and even ¬whether a university could ¬continue calling itself a university.
Mr Rogers, author of By Royal Appointment, Tales From The Privy Council, added: “University royal charters encourage ¬international researchers and students to the UK.”
Stephen Curry, Professor of Structural Biology at London’s Imperial College, warned: “The Bill places undue power in the hands of ¬government and erodes academic freedom.”
It is likely to be challenged in the House of Lords where many university ¬chancellors sit as peers.
The first royal charter was given to Cambridge University in 1231 by Henry III granting it the right to run its own affairs.
A spokeswoman at the Department for Education said: “UK Research and Innovation will ensure the UK is equipped to carry out more world-class ¬multidisciplinary research.
“All individual research councils will retain their autonomy, with individual funding streams and will continue to have authority on decisions within their discipline.”
A Buckingham Palace spokeswoman said: “We wouldn’t comment on the Queen’s ¬audiences with the Prime Minister.”