Friday’s announcement was the first indication about which players Nishino has in mind for the World Cup.
Japan fired Halilhodzic last month, only two months before the World Cup opens, and replaced him with Nishino.
Honda has seven goals with Mexican side Pachuca this season. The attacking midfielder, a mainstay on Japan’s recent World Cup squads, fell out of favor with Halilhodzic, who benched him during qualifying matches.
Borrussia Dortmund midfielder Kagawa, who has been struggling with injuries, was named for the first time since October.
Other Europe-based players include Leicester forward Shinji Okazaki and Bremen forward Yuya Osako.
In two World Cup warm-up matches, Japan will face Switzerland on June 8 in Lugano, Switzerland, and Paraguay on June 12 in Innsbruck, Austria.
Japan will be playing in its sixth straight World Cup, but has only twice reached the knockout round, losing both times in the last 16. It reached the last 16 in 2002 under French coach Philippe Troussier, and again in 2010 under Japanese coach Takeshi Okada.
Japan will play in Group H at the World Cup with Colombia, Poland and Senegal.