43-0 looks comfortable enough on paper but there were some unsettling moments for England who had to overcome losing players to a red and a yellow card on their way to victory.
Head Coach Mark Mapletoft will take the bonus point win but probably acknowledge that there is work to do in several areas if his side are to improve on last year's showing.
England struggled to assert their superiority in the early stages in testing, wet conditions in Tokyo.
The home team were aggressive in defence, understandably backed by a vociferous crowd, and handling mistakes were commonplace.
Gloucester's Dan Williams worked hard in the tight, carrying the ball around the fringes and clearing out rucks powerfully.
Bath flanker Josh Ovens got things going as he broke from inside in his own half and romped into the Japan half. The support wasn't quite there but England were patient and Ovens finished off the move after a couple more phases.
And the back row prominent again in England's second score as Chris York powered over from close range after a muscular break from the back of a set scrum from Carl Fearns.
Skipper Luke Eves led from the front as he took a great angle to score England's third just before the interval and England looked to be away with a 24-0 interval lead.
It was Eves' last contribution as he was replaced at half time by Gloucester's Henry Trinder and England started the second half in search of the bonus point try.
But things took an unexpected twist early in the second period as Quins prop Joseph Marler was sent off on the advice of the touch judge.
Understandably buoyed, Japan piled on the pressure but turned over ball near the England line and scrum half Ben Youngs broke and put winger George Lowe in for a sprint to the corner from his own 22.
England added a fifth as Fearns smashed his way over from a 5m scrum but were then reduced to 13 men as Bob Baker was yellow carded for slowing the ball down in a ruck.
With the game losing some fluency as the second half ebbed away, Trinder almost got on the scoresheet but was halted just short but Courtney Lawes took a flat pass to stroll through a gap and cross untouched.
Dave Lewis got a half hour run out as a second half replacement for Youngs and had a couple of worrying moments as he had kicks charged down in his own half which was perhaps understandable give the lack of forwards protecting him at the breakdown.
But his service out of hand looked slick and his confidence looked unaffected after a couple of sniping runs.
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