Softbank Mobile, the mobile phone unit of the Internet conglomerate, was a victim of its own success over the weekend as the glitch, caused by a swell of public interest, prompted criticism from rivals.
The Internal Affairs and Communications Ministry ordered the firm to study the cause of the problem.
Softbank, which entered the cutthroat sector recently by buying British giant Vodafone's Japanese operations, resumed the service Monday.
"We miscalculated the volume" of orders from subscribers, Softbank president Masayoshi Son told a news conference Monday. "We caused big trouble. I apologize for that."
Son said the company "doubled" the capacity of its system to transact orders from subscribers. He estimated the confusion cost hundreds of millions of yen (several million dollars) to the sprawling company.
Son, one of Japan's richest people who has built the Softbank empire, declined to comment on his potential responsibility for the system trouble.
"Risks always come up whenever we try something new," he said. "There is nothing like a 100 percent perfect system."
Industry leader NTT DoCoMo and second-ranked KDDI said they had agreed to lighten the burden on Softbank's system so as to allow Japan's new "number portability" -- which lets subscribers switch carriers.
NTT DoCoMo and KDDI issued statements Sunday severely criticizing Softbank for its failure to transfer customers, particularly those who want to switch to their rival services.
Softbank in April completed a mega-deal to buy Vodafone Japan for 15 billion dollars. It declared a new price war on the eve of the portability shake-up in an effort to grab customers away from NTT DoCoMo and KDDI.
Armed with a flashy media campaign, including television advertise