Imperial College London is bracing itself for a cut in funding when the research assessment exercise allocations are announced on 5 March.
Although Imperial's potential losses will be mitigated by a £50 million government fund earmarked for science, engineering, mathematics and medicine research, one vice-chancellor said: "There's no model that does not show (Imperial) losing money. The only question remaining is the amount."
One view in the sector is that the college's focus on becoming the UK's first academic health sciences centre (AHSC) led to some disappointing RAE results, which determine quality-related (QR) research funding.
Imperial was ranked 11th in Times Higher Education's Table of Excellence in cancer studies and fifth for cardiovascular medicine.
In 2007, Sir Ara Darzi, the Health Minister and professor of surgery at Imperial, called for National Health Service research to be led by AHSCs - university-hospital partnerships for teaching, research and clinical care.
Imperial became the first AHSC when its faculty of medicine merged with Hammersmith Hospitals and St Mary's NHS trusts to form Imperial College Healthcare NHS Trust in October 2007.
It may be that Imperial had been adversely affected by the time and effort required by the merger, the vice-chancellor said, but its research would gain in the long term.
"It's an experiment. We don't yet know the outcome," he said.
Staff have been ordered to prepare budgets for 2009-10 based on the assumption that they will receive 5 per cent less than in the 2008-09 budget year.
Sir Roy Anderson, rector of Imperial, said: "We are reassured to see that the Higher Education Funding Council for England is committed to safeguarding the share of mainstream QR grant allocated for research in science, engineering, medicine and mathematics, which are vital to the UK's competitive edge and its ability to take advantage of the economic recovery when it comes.
"Across all medical units of assessment, the college had the second-highest volume of world-leading research activity."