One of the world's leading particle physics instruments has been severely damaged in an accident.
On 12 November, one of the photomultiplier tubes exploded causing a chain reaction that resulted in most of the other 11,200 light detectors also blowing up.
Scientists say the accident is a major setback, as Super-Kamiokande has produced spectacular results, helping to answer long-standing questions about the Universe. Super-Kamiokande was the very first detector to establish that neutrinos can change into different types.
It was also one of the first detectors to help establish a mass for neutrinos.
'We will rebuild the detector'
Officials are still trying to determine what happened, and why the explosion of a single photomultiplier tube should have resulted in the destruction of most of the rest.
One British physicist told BBC News Online that he was puzzled why a single event could have such devastating consequences. "Questions should be asked," he said.
Commenting on the disaster the director of the observatory, Yoji Totsuka, said: "As a director of the Kamioka Observatory, which owns and is responsible to operate and maintain the Super-Kamiokande detector, it is really sad that I have to announce the severe accident that occurred on 12 November and damaged the significant part of the detector."
He added: "We will rebuild the detector. There is no question."
Big task
Koichiro Nishikawa, a spokesman for the K2K experiment, which uses the observatory, has released another statement.
He said: "On behalf of the K2K experiment, I thank all the concern expressed on the accident at Super-Kamiokande. K2K will fully support the Kamioka Observatory and will put the first priority on the recovery of Super-Kamiokande as early as possible."
Technically it is not very difficult to repair the detector but logistically it is a major problem.
50,000 tonnes of super-pure water will have to be pumped out and the debris from the shattered tubes removed. Then thousands of new detectors will have to be fitted and tested, and then the water replaced.
It is a task that will take at least a year. Officials say that they will take the opportunity to modify the detector, in particular to reduce the number of the photomultiplier tubes by about a half.
They say this will not affect the detector's performance and will make another mishap less likely.
The observatory achieved a major goal in 1998 when it found evidence that neutrinos can change from one type into another on their way through the Earth.
The main emphasis recently has been to study this phenomenon with neutrinos produced by an accelerator at the KEK laboratory, 250 kilometres from the Kamioka Observatory and beamed through the Earth towards it (hence the name K2K for the experiment).
The aim will be to resume this experiment as soon as possible, possibly within a year.
All images by ICRR (Institute for Cosmic Ray Research), The University of Tokyo