The Italian lamented the lack of intensity that his side showed after a positive start against Ivory Coast, suggesting they gave their opponents too much space
Keisuke Honda gave the Samurai Blue a 16th-minute lead but two goals in as many second-half minutes from Wilfried Bony and Gervinho earned three points for the West Africans.
Zaccheroni expressed his frustration at the manner in which his side surrendered the initiative and felt Japan did not play with sufficient dynamism after taking the lead, simply allowing the Elephants too much time and space.
"In general we started well and played dynamically in the opening stages," the 61-year-old told reporters after the game.
"As for what happened, Ivory Coast increased their strength and were able to beat us. It was true in the last 20 minutes of the first half as well, but we weren't able to attack them enough.
"We let them attack us when we should have played more aggressively. We gave their players too much space and didn't play well defensively or offensively.
"Ivory Coast won because they had space. Normally we can play quickly, but tonight we gave them too much room."
Japan now face Greece on June 19 and Colombia on June 24, with Zaccheroni insisting there is more to come from his team and they have not yet given up hope of progressing beyond the group stages.
"We have two games left and now we have to improve our morale," he continued.
"We have to play better than we did tonight, and if we can do that then we know we're capable of producing good results. The past is in the past; what's important is what's coming next.
"Normally we know what we have to do, and when we accomplish that our results are fantastic. Tonight we didn't just play an excellent opponent, but we didn't play to our standards."