The Queen will "hit the roof" if Theresa May follows through on plans to strip the UK's seven research councils of their royal charters.
The government is drawing up plans to amalgamate the seven bodies as the UK Research and Innovation without a charter.
Critics of the move, which is being overseen by the Universities minister Jo Johnson, believe it could lead to politicians becoming involved in scientific research.
Each year the councils invest around £3bn in research covering medical and biological sciences to astronomy, physics, chemistry and engineering. It also funds research into social sciences, economics, environmental sciences and the arts and humanities.
Constitutional expert David Rogers told the Mirror: "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."
Some of the best-known organisations to operate under the framework are the BBC, the Bank of England and the British Council. Once granted royal charters cannot be changed without government approval.
There are also fears the new Office for Students will override the academic independence of the 50 universities that have royal charters.
Announcing a green paper on the reform, Johnson said: "We must do more to ensure that the time and money students invest in higher education is well spent. Our ambition is to drive up the quality of teaching in our universities to ensure students and taxpayers get value for money and employers get graduates with the skills they need.
"The new Office for Students would have a clear remit to champion value for money and the student interest in its decision-making. And by opening up the sector to new universities and colleges, students will have more choice than ever when they come to apply to university."