Keith Earls, Dan Leavy and Jack Conan all touched down twice, with Garry Ringrose scoring the other Irish try.
Paddy Jackson kicked five conversions and a penalty for a 100% record, with Rory Scannell adding a late conversion.
Japan trailed 31-3 at the break but second-half tries by Ryuji Noguchi, Kenki Fukuoka and Yutaka Nagore gave the final scoreline a flattering look.
Rikiya Matsuda added the extras to two of the hosts' three scores, but his side were outclassed for most of the match, Earls and Conan both impressive and Leavy, Quinn Roux and Cian Healy among those taking advantage of their opportunity to impress in the absence of 11 Ireland players away on Lions duty.
The two teams were meeting for the first time in 12 years, Ireland having won their five previous encounters.
The match was played at the Shizuoka Ecopa Stadium, one of the venues for the 2019 Rugby World Cup, for which Ireland and Japan have been drawn together in Pool A, along with Scotland and two other teams yet to be confirmed.
Japan, ranked 11th in the IRB rankings and seven places below their opponents, have earned a growing reputation on the international stage, precipitated by their famous win over South Africa in the World Cup in September 2015.
The Cherry Blossoms beat Romania 33-21 last weekend, but knew they would face a stiffer test at the hands of Joe Schmidt's charges, who comfortably saw off USA Eagles 55-19 seven days ago.
For Ireland, centre Scannell, winger Andrew Conway and scrum-half Luke McGrath were handed their first international starts, while Jackson replaced Joey Carbery, whose tour was ended by an ankle injury sustained in the victory in New Jersey.
Ireland belied the 27C temperatures to produce an energetic first-half performance, Ulster fly-half Jackson controlling proceedings and giving them an early lead with a penalty.
In-form winger Earls scored the first try of the game in the 11th minute, cantering down the left to touch down after Ireland won possession from a Japanese scrum and Conan made the break, before off-loading to the Munster man.
Yu Tamura landed a penalty to reduce the home side's deficit but the visitors took full advantage of Heiichiro Ito's sin-binning by adding three more tries before the interval.
Leavy rumbled over for his first international try on his fourth appearance after Quinn Roux won lineout possession and Devin Toner fed his fellow Leinster forward.
The flanker crossed again three minutes later after another successful lineout created the platform for Earls to engineer a clever line break, running into empty space and sidestepping two defenders before off-loading to Leavy.
As Ireland continued to dominate the breakdown, Conan grabbed his first try by crossing in the corner after the ball went quickly through the Irish hands and the ubiquitous Earls provided the final pass.
Conan again provided the finish soon after the restart, picking up the loose ball after a cheap turnover, kicking through and dotting down for a comfortable try to extend the tourists' lead.
Conway missed 10 minutes of action when receiving a yellow card for a high tackle and Japan scored their first try from their best passage of play on the hour, Noguchi shrugging off a couple of attempted tackles to surge over.
Ringrose completed a fine Irish move by dancing round a tired looking Michael Leitch to dive over in the corner, then Earls ensured a try double for the second successive game by darting over after prop Dave Kilcoyne had shown pace to surge almost 40 metres to within a couple of the line.
Japan showed some belated creative spark, aided by a porous Irish defence, to notch late tries through Fukuoka and Nagare, but Jamie Joseph's side will look for improvement when the sides clash again next week.
Japan: R Noguchi; K Matsushima, W Tupou, D Carpenater, K Fukuoka; Y Tamura, F Tanaka; K Inagaki, S Horie (capt), H Ito; K Inagaki, S Horie (capt), H Ito; K Yatabe, U Helu; M Leitch, Y Tokunaga, A Lelei.
Replacements: Y Niwai, S Ishihara, T Asahara, H Tui, S Matsuhashi, Y Nagare, R Yamanaka, R Matsuda
Ireland: S Zebo; A Conway, G Ringrose, R Scannell, K Earls; P Jackson, L McGrath; C Healy, N Scannell, J Ryan; Q Roux, D Toner; R Ruddock, D Leavy, J Conan.
Replacements: J Tracy, D Kilcoyne, F Bealham, K Treadwell, J O'Donoghue, K Marmion, R O'Loughlin, T O'Halloran.
Ireland ran in seven tries as they secured a convincing win in the first of two Test matches against Japan.