The Samurai Blue secured a hard-fought 4-3 friendly win over Zambia on Friday night, which handed them their third victory on the trot.
However, Japan had to rally from two goals down against Zambia – a team ranked 30 spots below them – to secure the win in Tampa.
Honda scored two goals from the penalty spot while Shinji Kagawa's strike also helped reduce the deficit. Yoshito Okubo then netted an incredible stoppage-time effort to secure the win.
While Japan travel to the World Cup in a good run of form, Honda has admitted that his team’s vulnerability at the back and their inability to control matches could be their downfall in Brazil.
"Just like the last match [3-1 win over Costa Rica] we allowed the other team to score the first goal, and that's still a big issue for us to deal with,” Honda told TV Asahi after the game.
“As for how we carried the match, we allowed them [Zambia] to control the initiative many times over 90 minutes and that's not good.
“We have to figure out what went wrong before the next match. I can't say exactly what happened without looking at the video.”
AC Milan's Honda and Manchester United's Kagawa will be vital to Japan's hopes of progressing from Group C, where they will face the Ivory Coast, Greece and Colombia.
And Honda revealed that he hoped his preparations for football’s biggest tournament would pay off.
"I've done a lot in order to compete in this World Cup, but there's still the last bit of preparation. I have to focus on my job and perform well,” he said.
Japan start their World Cup campaign against the Ivory Coast on June 14 in Recife.