NHS England say letters it sent to health bosses suggesting funding could be cut for the care of patients taking part in drug trials were "incorrect".
The letters were sent in the London region and referred to the "current financial climate".
But NHS England now say it will fund excess treatment costs and said the letters are being withdrawn.
Cancer Research UK said it "makes no sense" for the NHS to say it cannot afford to support the charity's research.
A spokesman for NHS England confirmed the letter said: "I am sure you will appreciate that in the current financial climate, the primary call for resources is to support clinical service provision for established service priorities.
"To this end, the NHS England London Region Area Team is unable to identify any uncommitted resources which could be used to support ETCs for clinical trials."
Shadow Health Secretary Andy Burnham said the contents of the letter, if correct, would have "devastated" medical research.
He told BBC News: "I am not sure at all that that is right. The letter is very authoritative. It refers to a new national policy in terms of the funding of drug trials. I don't think a letter like that is just sent out casually.
"This could have affected thousands of very poorly patients. It would have devastated medical research in the UK - major implications. I don't think somebody just sends a letter like that casually."
Professor Peter Johnson, Cancer Research UK's chief clinician, said: "The partnership between the NHS and organisations which fund research, such as Cancer Research UK, has been a great success story.
"We lead the world in being able to offer patients participation in clinical trials, but all this will be undone if the NHS cannot keep its side of the bargain.
"Taken overall our trials save the NHS money by providing free treatments in many cases, and it makes no sense for the NHS to claim that it cannot afford to support our research. It cannot afford not to do so, for patients, for the NHS and for the wider UK economy."
A spokesman for NHS England said: "We strongly support medical research and we will fund excess treatment costs in line with the national rules, so these local letters were incorrect and are being withdrawn."