According to an article¹ from Mainichi Interactive, domestic Air Traffic Control in Japan delayed many flights for a period of 54 minutes while a computer "glitch" that caused flight information to disappear from ATC screens.

The planes themselves didn't disappear, so there was little concern over safety, but as a precaution, new flights were slowed substantially or stopped; and the controllers were required to contact each plane individually to reconfirm their information.