Two separate incidents have emerged in which patients have been told they were put at risk of contracting Creutzfeldt-Jakob Disease (CJD).
In both cases the fatal brain-wasting disease could have been picked up during surgery.
At Queen's Hospital in Romford in Essex, 21 brain surgery patients have received letters.
A further 38 patients in Wales were told on Saturday they had been put at risk.
Self employed builder, Paul Davey who attended the hospital in Romford said: "Worry just runs away with you doesn't it, the what ifs, there's no treatment, no cures, so if it comes - that's it.
"When you show people the letter... well its like well it's only a small chance, but imagine if your name was on the letter. It's alright when it's someone else's name."
Mr Davey received a letter from his hospital telling him that the mother of a patient who had an operation in the same operating theatre had developed an inherited form of CJD.
That patient had then been tested, and found to be carrying a gene that meant she too could go on to develop the disease.
The letter said his risk was thought to be extremely small, but that he should protect public health by not donating blood, organs or tissues.
"If the chances were that small why did they send the letter? I'd be better not knowing. You can't tell someone that they can't give blood or visit a dentist and then tell them it's not serious," Mr Davey told the ´óÏó´«Ã½'s Newsnight programme.
The other incident was at a hospital in Wales. In this case, Public Health Wales is not revealing the name of the hospital, nor the type of surgery involved.
In both situations, the hospitals say they followed normal practices to clean, disinfect and sterilise the surgical instruments involved.
One of the UK's leading experts on prion diseases, Professor John Collinge, said such incidents are not uncommon.
He said the risk to patients from contaminated surgical instruments was believed to be small but is not yet quantified. He thought more could be done to stop this happening at all.
His team has developed an effective prion deactivation soak, a bit like a biological washing powder, and even has a commercial partner, but the substance is not being used in hospitals.
"I am surprised this hasn't been picked up," Prof Collinge told Newsnight. "It's concerning as a clinician to hear that patients are continuing to be notified they might have been exposed to contaminated instruments when we thought several years ago this problem was solved...
"Clearly it takes time to change practice in hospitals but I am concerned this hasn't been taken up more speedily."
Conservative MP, Sir Paul Beresford, is seeking an adjournment debate on the issue on Wednesday. He is concerned about a lack of action by the Department of Health and whether worries about extra cost might explain why these technologies were not in use.
"I think if the hospitals were under pressure and the cleaner was provided at a commercially viable cost - which I think would be low if they had a huge market ie every single hospital in the country - then the costs would be lower.
"The other side of cost is prevention - prevention of having these absolutely mortified people getting these horrendous notices saying they are at risk.
"I want the DoH to go back to the commercial firms and give them the light to go ahead by explaining to them that they intend them to have the commercial market - that will inspire them to do the final tests and changes to make it more viable for the hospitals to use."
CJD is one of a group of so-called prion diseases. Unlike viruses and bacteria, prions are extremely hardy, and cannot be destroyed by normal decontamination methods, such as autoclaving of surgical instruments.
Newsnight has discovered that in the aftermath of the BSE, or "mad cow", incident in the UK, several research teams produced prion deactivation techniques.
The human form of BSE, or variant CJD, is another of these prion diseases. The research groups had even teamed up with commercial companies, keen to develop these decontamination products.
Professor Collinge's team worked with Dupont. Another was a spin out from Edinburgh University, and a third emerged from the government-sponsored Health Protection Agency (HPA). But all three products seem to have quietly disappeared before they could be proved in a hospital setting.
Edinburgh University told Newsnight: "It is believed that end users would only be prepared to adopt (our method) if legally required to do so."
The HPA said there was "no incentive for hospitals to use it. We did the research and development, but we don't set the policy". They referred us to the Department of Health.
Professor Collinge added: "The DoH doesn't now give central diktats to NHS trusts... it is frustrating things don't seem to be joined up.
"We spend a lot of money on ensuring bloods are safe as possible in this country but we seem to be doing relatively little with surgical instruments, and that doesn't seem entirely logical."
The DoH said technologies to improve hospital infection control go to its Rapid Review Panel (RRP).
The product from Professor Collinge's group was deemed to have potential, but he was told that more work was needed in a clinical setting.
The company was given advice on how to improve the application in September 2010 and it's now up to the manufacturer to decide whether to take it further.
Dupont says it made a business decision to withdraw its prion deactivator some time ago, and doesn't want to comment further.
