Clinton, on a brief visit to disaster-hit Japan to show US solidarity, took the unusual step of kissing Empress Michiko on the cheek. She shook hands with Emperor Akihito, and was not seen bowing.
President Barack Obama's bow before the emperor during a 2009 visit enraged his conservative critics, who said the US leader should stand tall, although officials insisted that bowing was customary.
The emperor and empress, figureheads of Japan under the post-World War II constitution, are traditionally reticent in public.
But the emperor appeared on live television for the first time after the March 11 megaquake, and the imperial couple also visited victims of the tragedy.
Deccan Herald is on WhatsApp Channels| Join now for Breaking News & Editor's Picks