"You won't be seeing Mr. Iwata at E3 next week. He's been instructed by his physician not to travel overseas in the immediate future, and so he will not be making the trip to Los Angeles," the representative said. "Please understand that it is business as usual for Mr. Iwata, and he continues his normal duties as president of Nintendo Co., Ltd. while he remains in Japan. As always, he will be actively involved in all of Nintendo's activities at the show."
Source: http://www.gamespot.com/articles/nintendo-president-not-coming-to-e3-on-doctor-s-advice/1100-6420132/