Staff at the store said the glitch had apparently been caused by the volume of people overloading the system.
Apple fans across Asia queued for hours to get their hands on the new iPhone, looking to be the first to own a gadget the company hopes will be as big a worldwide smash as the iPod.
More than 1,000 people, many waiting through the night, besieged a store in downtown Tokyo as the iPhone went on sale for the first time in Japan, where having the latest gizmo is almost a national obsession.
Some Japanese began camping out days before the launch for the thrill of being the first to buy the new smartphone -- described as twice as fast and half as expensive as the original iPhone, which was never sold in Japan.