The team found that the soils were moving at a rate of up to one centimetre a month.
A leading archaeologist has accused the Peruvian Government of failing to act on a report that suggests the ancient Inca citadel of Machu Picchu is in danger of falling off its mountain perch.
According to the Japanese, there are alarming signs that the mountainside beneath the 2,250-metre-high city could give way in a potentially catastrophic landslide within the next few years.
"Machu Picchu is constructed over a place that is moving inside. It's terrible," Dr Kauffmann said.
"According to the Japanese, this phenomena is going now very quickly, so if we follow the Japanese, in five, 10 or perhaps 15 more years, we won't have Machu Picchu any more."
Geological activity
To study the geological activity in the mountain, the researchers from the Disaster Prevention Research Institute at the Kyoto University set up sensitive instruments buried in the steepest slopes around the citadel.
The team found that the soils were moving at a rate of up to one centimetre a month.
The team later published an annex to their study which acknowledged that the movement was exaggerated by excessive rainfall and construction work at a hotel beneath the site in the months that they were there, but their concerns remain.
And at the site its self, there are clear signs of problems. The Incas were master stone-masons, crafting walls out of massive blocks of granite so tight fitting that it is impossible to slip a piece of paper between them.
But gaps have begun to appear in some of the constructions, hinting at movement beneath.
Warning signs
All around the spectacular razor-back ridge that the Incas built on, there are other warning signs: deep scars on the jungle-clad slopes left by landslides caused by natural erosion in the geologically young Andean mountains.
The mountain perch where the Incas established their homage to the gods of the Sun and the Moon is also split by no less than five geological faults.
The original inhabitants managed to stabilise most of these, even turning some into drainage channels, but they remain weak spots in the constructions, and most of the damage to buildings lies along those lines.
The National Institute of Culture which administers Machu Picchu acknowledges the problem, but it insists there is no need for panic.
"This is nothing new," said the Institute's executive director Ricardo Ruiz.
"The Incas were aware of just how unstable the region was when they started building 500 years ago. They were careful to protect the city when they built the foundations, and they did such a good job that there's very little damage to Machu Picchu until now," he added.
'Alarmism' danger
Mr Ruiz also attacked experts like Dr Kauffmann for being alarmist. "The geological process takes a very long time, and Dr Kauffmann knows this. In reality it takes 10 or 15 years to properly diagnose what's going on," he said.
"So for us to take radical action after a study that lasts just two or three months would be irresponsible," he added.
The Institute insists that it is determined to protect the spectacular ruins. Machu Picchu draws in some 700,000 tourists each year, easily winning the prize as Peru's biggest draw-card.
The Institute has plans to increase the numbers to nearly two million by 2005, and says it simply cannot afford to see anything happen to the site.
But Dr Kauffmann believes the institute is simply burying its head in the sand.
"I think the National Institute of Culture is acting irresponsibly. The solution isn't to hide the problem but to confront it, to see if the Japanese are right," he said.
"If they are not right, then we are okay, but maybe they are right. We can't afford to ignore them," he added.