Visiting captain Rhys Ruddock was happy to get the win but said there were areas for improvement ahead of the second test next Saturday.
"It was really tough, really physical at times," he said on the IRFU website. "We're happy with the way we started and Japan probably didn't show how well they can play. But they finished strongly, and for next week we'll have to be a lot better.
"We'll have to tighten up our defence and play a bit better kicking game as well."
Despite several regulars away on duty with the British and Irish Lions in New Zealand, Ireland had little trouble against a disappointing Japanese side, with Keith Earls, Dan Leavy and Jack Conan all crossing twice before Garry Ringrose touched down later in the second half.
Ireland blew the game wide open early on after Japanese tighthead prop Heiichiro Ito was sent to the sin bin for killing the ball following a series of infringements, compiling 21 points with the extra man.
Japan applied some late pressure and scored three tries in the closing 20 minutes through Ryuji Noguchi, Kenki Fukuoka and Yutaka Nagare.
(Writing by Peter Rutherford; Editing by Sudipto Ganguly)
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