Alberto Zaccheroni's side have reached the last four World Cup finals but their coach warned the Blue Samurai not to expect qualification to be a formality.
They got off to a good start on Sunday, Keisuke Honda putting them ahead after 12 minutes.
Two goals in three second-half minutes from Ryoichi Maeda and Shinji Okazaki completed the scoring in the Group B clash.
Japan now host Jordan on Friday before travelling to Brisbane where they face a tough match against Australia on June 12.
The other game in the group saw Jordan and Iraq share a 1-1 draw.
A trademark long-range strike from Nashat Akram gave the visitors the lead in the 14th minute but Jordan equalised two minutes before half-time when keeper Mohammed Kassid fumbled Baha Suleiman's long-range shot into the path of Ahmad Ibrahim, who finished from close range.
In Group A, Iran produced a late sucker punch to snatch an ill-deserved 1-0 win in Uzbekistan.
The hosts dominated the game but failed to take their chances and Mohammad Khalatbari rounded off a 94th-minute counter-attack with a calm finish to rub salt in their wounds.
Elsewhere in the group, Qatar recorded a 1-0 win at Lebanon courtesy of Sebastian Soria's 64th-minute strike.
Sunday's AFC 2014 World Cup Qualifying Results
Uzbekistan 0-1 Iran
Lebanon 0-1 Qatar
Japan 3-0 Oman
Jordan 1-1 Iraq