The scientists who appeared to have found in September that certain subatomic particles can travel faster than light have ruled out one potential source of error in their measurements after completing a second, fine-tuned version of their experiment.

Their results, posted on the ArXiv preprint server on Friday morning and submitted for peer review in the Journal of High Energy Physics, confirmed earlier measurements that neutrinos, sent through the ground from Cern near Geneva to the Gran Sasso lab in Italy 450 miles (720km) away seemed to travel faster than light.

The finding that neutrinos might break one of the most fundamental laws of physics sent scientists into a frenzy when it was first reported in September. Not only because it appeared to go against Albert Einstein's theory of special relativity but, if correct, the finding opened up the troubling possibility of being able to send information back in time, blurring the line between past and present and wreaking havoc with the fundamental principle of cause and effect.

The physicist and TV presenter Professor Jim Al-Khalili of the University of Surrey expressed the incredulity of many in the field when he said that if the findings "prove to be correct and neutrinos have broken the speed of light, I will eat my boxer shorts on live TV".

In their original experiment scientists fired beams of neutrinos from Cern to the Gran Sasso lab and the neutrinos seemed to arrive sixty billionths of a second earlier than they should if travelling at the speed of light in a vacuum.

One potential source of error pointed out by other scientists was that the pulses of neutrinos sent by Cern were relatively long, around 10 microseconds each, so measuring the exact arrival time of the particles at Gran Sasso could have relatively large errors. To account for this potential problem in the latest version of the test, the beams sent by Cern were thousands of times shorter – around three nanoseconds – with large gaps of 524 nanoseconds between them. This allowed scientists to time the arrival of the neutrinos at Gran Sasso with greater accuracy.

Writing on his blog when the fine-tuned experiment started last month, Matt Strassler, a theoretical physicist at Rutgers University, said the shorter pulses of neutrinos being sent from Cern to Gran Sasso would remove the need to measure the shape and duration of the beam. "It's like sending a series of loud and isolated clicks instead of a long blast on a horn," he said. "In the latter case you have to figure out exactly when the horn starts and stops, but in the former you just hear each click and then it's already over. In other words, with the short pulses you don't need to know the pulse shape, just the pulse time."

"And you also don't need to measure thousands of neutrinos in order to reproduce the pulse shape, getting the leading and trailing edges just right; you just need a small number – maybe even as few as 10 or so – to check the timing of just those few pulses for which a neutrino makes a splash in Opera."

Around 20 neutrino events have been measured at the Gran Sasso lab in the fine-tuned version of the experiment in the past few weeks, each one precisely associated with a pulse leaving Cern. The scientists concluded from the new measurements that the neutrinos still appeared to be arriving earlier than they should.

"With the new type of beam produced by Cern's accelerators we've been able to to measure with accuracy the time of flight of neutrinos one by one," said Dario Autiero of the French National Centre for Scientific Research (CNRS). "The 20 neutrinos we recorded provide comparable accuracy to the 15,000 on which our original measurement was based. In addition their analysis is simpler and less dependent on the measurement of the time structure of the proton pulses and its relation to the neutrinos' production mechanism."

In a statement released on Friday, Fernando Ferroni, president of the Italian Institute for Nuclear Physics, said: "A measurement so delicate and carrying a profound implication on physics requires an extraordinary level of scrutiny. The experiment at Opera, thanks to a specially adapted Cern beam, has made an important test of consistency of its result. The positive outcome of the test makes us more confident in the result, although a final word can only be said by analogous measurements performed elsewhere in the world."

Since the Opera (Oscillation Project with Emulsion-tRacking Apparatus) team at Gran Sasso announced its results, physicists around the world have published scores of online papers trying to explain the strange finding as either the result of a trivial mistake or evidence for new physics.

Dr Carlo Contaldi of Imperial College London suggested that different gravitational effects at Cern and Gran Sasso could have affected the clocks used to measure the neutrinos. Others have come up with ideas about new physics that modify special relativity by taking the unexpected effects of higher dimensions into account.

Despite the latest result, said Autiero, the observed faster-than-light anomaly in the neutrinos' speed from Cern to Gran Sasso needed further scrutiny and independent tests before it could be refuted or confirmed definitively. The Opera experiment will continue to take data with a new muon detector well into next year, to improve the accuracy of the results.

The search for errors is not yet over, according to Jacques Martino, director of the National Institute of Nuclear and Particle Physics at CNRS. He said that more checks would be under way in future, including ensuring that the clocks at Cern and Gran Sasso were properly synchronised, perhaps by using an optical fibre as opposed to the GPS system used at the moment.

This would remove any potential errors that might occur due to the effects of Einstein's theory of general relativity, which says that clocks tick at different rates depending on the amount of gravitational force they experience – clocks closer to the surface of the Earth tick slower than those further away.

Even a tiny discrepancy between the clocks at Cern and Gran Sasso could be at the root of the faster-than-light results seen in September.