The problem affected a cooling system for high-powered magnets designed to steer beams of particles around the Large Hadron Collider's 27-kilometre (16.9-mile) circular tunnel, CERN said.
The LHC "is still in commissioning phase, it's a very complex tool and it's normal for there to be stoppages," a CERN spokeswoman told AFP.
Commissioning work stopped on Wednesday, but was likely to resume later Thursday, she said.
The LHC took nearly 20 years to complete and at six billion Swiss francs (3.76 billion euros, 5.46 billion dollars) is one of the costliest and most complex scientific experiments ever attempted.
It aims to resolve some of the greatest questions surrounding fundamental matter, such as how particles acquire mass and how they were forged in the "Big Bang" that created the Universe some 13.7 billion years ago.
Counter-rotating beams, comprising strings of protons, are whizzed around the tunnel and then are smashed together in four huge laboratories.
Arrays of detectors swathing the walls of these chambers will trace the sub-atomic rubble spewed out from the collision, looking for signatures of novel particles.
The September 10 switch-on saw the testing of a clockwise beam, and then an anticlockwise beam. The first collisions are not expected for a number of weeks, given the long process of testing the LHC's equipment.
The steering magnets in the LHC tunnel are chilled to as low as -271 degrees Celsius (-456.25 degrees Fahrenheit), which is close to absolute zero and colder than deep outer space.
At this extreme temperature, electrical currents overcome resistance, thus making it easier and cheaper to power electro-magnets.


Usually, light beams shine in a straight line, with the possible exception of light being bent by gravity. But scientists are now investigating how to make light beams into looped and knotted configurations. The possibility for these structured light beams arises from some curious solutions to Maxwell’s equations, which describe the fundamentals of electricity and magnetism.
Now a team from the jet propulsion laboratory in California have found another anomaly which seems to appear when some spacecraft make a flyby of earth. For examble when the NEAR spacecraft flew past the earth on its way to visit an asteroid, it left moving at 13mm/s slower than it should have done, and the Galileo probe was speeded up by 4mm/s these are tiny effects as the probes are moving more than a million times faster than this, but it is well within our ability to measure their speeds.