Tuilagi scored his first try in the third minute and gave Samoa a commanding 15-0 lead midway through the first half with his second after some poor one-on-one tackling from the hosts.
Full-back James So'oialo's conversion widened the lead to 17-0 lead. Japan weren't helped by some poor goal-kicking as they missed two early penalties and it wasn't until the 20th minute that they finally got on the scoreboard with a try by Koliniasi Ryu Holani who crashed over from five metres out.
Manaia Salavea ran in Samoa's third try in the 34th minute and So'oialo's third conversion gave the visitors a solid 24-8 lead at half time.
A far better performance in the second half saw Japan close to 24-15 thanks to a good try by Takehisa Usuzuki as the Japanese backs finally stretched the Samoan defence to give the crowd of 9,700 something to cheer about.
With Japan camped on the Samoan line for an extended period it seemed Kirwan's team were about to get within a score of the Samoans. But they were unable to turn all that pressure into points, with at least three tries missed when the final pass failed to go to hand.
George Pisi scored rubbed salt into the wound by scoring against the run of play in the 59th minute as Samoa ensured there was no way back for Japan.
All but Saturday's match in this year's tournament were moved from Japan to Fiji because of the March 11 earthquake and tsunami.
Earlier on Saturday, Tonga upset Fiji 45-21 in the opening match in Lautoka.
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