Ministers will enshrine into law the idea that there should be no political interference in research funding.
The concept, known as the Haldane Principle, has been a guiding precept for science spending but never a requirement until now.
The move follows concerns that a proposed shake-up would lead to the centralised funding of research.
Parliament is considering new laws that would see the formation of a new body to oversee spending on science.
The Universities and Science Minister Jo Johnson said that the changes to the Higher Education and Research Bill he was proposing would guarantee the independence of scientific research
"The amendments announced today demonstrate the government's commitment to the Haldane Principle and decisions on individual proposals should be reviewed and made by experts in their fields."
Currently, UK research is funded by nine separate organisations. Each body specialises in specific fields.
The system is regarded as one that works well and has contributed to Britain leading the world in many areas of science.
The government is proposing the creation of a new body called UK Research and Innovation (UKRI), which will oversee and co-ordinate the work of the research organisations, following a review of the system by Prof Sir Paul Nurse.
Critics of the reform fear that the restructuring is a merger in all but name. It would, they believe, lead to the loss of the close relationships between specialist funding bodies and research groups that has led to a system of effective funding that nurtures world class research.
To address these concerns Mr Johnson has decided to incorporate the Haldane Principle into law. He has also proposed amendments that require ministers or UKRI executives to consult with stakeholders before making any changes to the research focus or names of the current research councils
They also require the Secretary of State to make each council's separate budget allocation clear when issuing grants so that UKRI leaders can't divert money to their favoured projects.
The amendments also state that one of the research agencies that funds business research and development, Innovate UK, should maintain its focus in the industrial arena
Sarah Main, Executive Director of the Campaign for Science and Engineering, welcomed the proposed changes.
"I'm pleased to see the government adopting some substantive points raised by the science community and the House of Lords. It's a reassuring sign for the relationship between UKRI, government and scientists going forward."
"There remain some issues which we hope will be clarified through these amendments or later, for example enacting the interdisciplinary function of UKRI, consultation across the constituent bodies in forming UKRI strategy, and robust processes for UKRI and the Office for Students to work closely on the cross-over between university teaching and research."
Follow Pallab on Twitter.