The Department of Health has approved proposals from the Health Research Authority to streamline clinical trials, but experts have argued that more work is needed within the NHS to fast-track trials in an emergency.
They say that an emerging infection like bird flu, Sars or pandemic flu can spread across Britain and burn itself out within eight weeks.
But doctors hoping to test drugs or other treatments for patients can face delays of more than a year before they can recruit a single case to a trial.
It means doctors have little hope of learning which treatments are effective during an outbreak because patients will have recovered or died before the trial can start.
Calling for an overhaul, Farrar said the emergency trials needed to start within 24 hours of an epidemic emerging.
“Getting this information early on is critical to inform what we do and how we treat patients. Without it we are completely in the dark,” he said.
Pandemic flu is regarded as the most serious emergency risk that Britain faces, but other infections, including drug-resistant diseases, are also a serious threat.
Clinical trials need approval from the NHS and other bodies before doctors can recruit patients, but the process faces delays at almost every stage.
Researchers must apply for grants, submit study protocols and patient consent forms, gain ethical approval, find hospitals with the right facilities, equipment, supplies, staff and patients and then sign legal agreements with them all.
The long-winded process is designed to be thorough to protect patients and hospitals from litigation. Trials can go seriously wrong, as happened in 2006 when six young men nearly died in a drug trial at Northwick Park hospital in north London.
The 2002 Sars pandemic killed 774 people and infected more than 8,000 but had the virus not been contained it could have killed far more, experts said.
The reason the death toll was not higher was that patients were most infectious when they were most sick, so isolating the ill stopped the virus spreading.
“There is no doubt we were very lucky with Sars,” said Farrar. “But nobody knows where it has gone and we don’t have a vaccine. If it were to come back tomorrow and I got infected, the doctor treating me wouldn’t have a clue which drug, if any, to give me.”
A 2011 report from the Academy of Medical Sciences (AMS) raised major concerns about delays to clinical trials. It quoted Cancer Research UK data that found the typical time taken to launch a trial and treat the first patient was 621 days.
Sir Michael Rawlins, president of the Royal Society of Medicine, who chaired the report, said progress was disappointing. “It’s going in the right direction, but it’s painfully slow,” he told the newspaper.
The Health Research Authority was set up in response to the AMS report to streamline approval times. It means a simple trial could be approved within 25 days but the authority is aiming to approve emergency trials within 24 hours.
Farrar said he wanted more trials pre-approved so that doctors can start emergency tests in patients the moment an outbreak is identified.
“We need generic protocols which have been pre-approved by ethics committees and institutions at a national level,” he told the newspaper.
“All the information, from what samples to take to the forms we’d record patient data on, would be openly available. Then, in an emergency, a group that has worked on the top three or four interventions can start enrolling patients within 24 hours.
“There are groups trying to address this, but it’s nowhere near there yet.”