CSKA Moscow star Honda missed training on Tuesday after hurting his right knee in a league match against Spartak Moscow on Sunday while Kawasaki Frontale midfielder Nakamura misses out after breaking a toe, the JFA said.
Honda, 25, played a star role for the Blue Samurai in the 2010 World Cup in South Africa, scoring against Cameroon and Denmark in the group stages and picking up man-of-the-match awards in both games.
Nakamura, 30, had been called up for the first time since October last year, with national coach Alberto Zaccheroni saying the midfielder deserved a place in the squad after making a return to form in the J-League.
The JFA has not yet decided on replacements for the injured men.
Japan will play DPR Korea at the Saitama stadium on Friday and then Uzbekistan away on September 6 in the third Asian qualifying round for the 2014 World Cup in Brazil.