The Italian said on Tuesday he would wait to see if Inter Milan defender Nagatomo and CSKA Moscow midfielder Honda were able to play in Niigata after jetting in earlier in the day.
"Concerning the three players who arrived this morning, I have not made a decision on whether they will play a part," he said, including Dutch-based defender Maya Yoshida.
Zaccheroni has put 19-year-old striker Takashi Usami's senior debut on ice for Japan's first full international since the deadly earthquake and tsunami in March.
"He has huge talent for someone of his age but it's difficult to judge after two days of training," Zaccheroni said of the highly-rated Usami, who has been linked with a move to Bayern Munich.
"He has tremendous potential but how far he improves will be down to his work ethic. But I called him into the squad to get to know him better."
Usami had to be coaxed into training sessions by senior players after skulking on the sidelines playing "keepy-uppy" with himself at the start of Japan's camp.
"It was a little hard to get involved at the start," he admitted. "But the players helped me get and I try not to stay in my room. I want to mix and get used to the set-up."
Zaccheroni has called up 11 Europe-based players for the three-nation Kirin Cup, also involving the Czech Republic. The Czechs meet Peru on June 4 in Nagano.
Asian champions Japan face the Czechs in the tournament's final game on June 7 in Yokohama.
Both visiting teams agreed to travel to Japan after being given assurances that the nuclear crisis raging north of Tokyo posed no risk of radiation exposure to players and officials.
