The AC Milan playmaker was Japan's driving force in the Group E encounter but Shinji Okazaki and Shinji Kagawa were among those that struggled in front of goal in the draw with opponents ranked 154th by FIFA.
While Singapore goalkeeper Izwan Mahbud produced a brilliant performance to stymie the four-times Asian champions, the 57,000 fans at Saitama Stadium were unhappy with the Japanese effort and booed their disapproval at full time.
"The result was what it was, so there’s nothing we can do about it (the booing)," Honda was quoted as saying by Japanese media. "If anything, I think they took it easy on us.
"Someone needed to show a bit more individual quality and score. Not all of the shots we put in were easy shots and Singapore did well to keep us at bay. It was a combination of both that led to the result."
Honda dismissed suggestions the game had a similar feel to the Asian Cup quarter-final against United Arab Emirates in January where Japan were beaten on penalties despite dominating and creating numerous chances.
But critics will say it is another case of pretty build-up football from Japan without the ruthlessness in front of goal that sets the best teams apart.
Okazaki has notched more than 40 international goals and has scored in each of Vahid Halilhodzic's three friendly wins since the Franco-Bosnian was appointed coach in March but he was guilty of some poor finishing against Singapore.
Halilhodzic said his forwards lacked calmness in front of goal.
"We did everything possible to win. We didn’t put our chances away and perhaps we were a bit flustered in front of goal, and then there were the great saves by the goalkeeper," the former Algeria and Ivory Coast boss said.
"There is no magic in football, only hard work. The reality is that you have to score goals."
(Writing by Patrick Johnston in Singapore; Editing by Peter Rutherford)
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