"In attack we are not quite there yet," the AC Milan playmaker was quoted as saying by Kyodo News.
"Looking at the flow of the game we should have scored more. We had plenty of chances to. We lacked power and precision."
Japan were held to a shock goalless draw in Saitama by Singapore in their opening Group E match in June and also encountered striker issues before dispatching lowly Cambodia 3-0 at home last month.
More troubles came on Thursday, with Syria pushing for the opening goal early before fading in the second period.
Shinji Okazaki, fouled to win the opening penalty, notched a second after good work by Shinji Kagawa down the right, with substitute Takashi Usami completing the scoring late on after a neat Honda flicked assist.
Skipper Makoto Hasebe said Japan should have done better.
"It was good that we came out 3-0 winners in a tough game," he said.
"We had to make adjustments at halftime so we can't be satisfied."
Japan are not in World Cup action again until they play away to Singapore next month. While their group rivals play again on Tuesday, the Samurai Blue will face off against World Cup finalists Iran in a friendly in Tehran.
Japan boss Vahid Halilhodzic said the clash would be a tough test for his team.
"They are a much stronger team (than Syria) and are better than us," the former Algeria and Ivory Coast boss said.
"I've heard there will be a crowd of 80,000. It will be a completely different game."
(Writing by Patrick Johnston in Singapore; editing by Amlan Chakraborty)
