[2] In order to stand out from other fighting games, Team Ninja focused on making Dead or Alive provocative.

Team Ninja would in 2014 also collaborate with Omega Force on the development of Hyrule Warriors, an action game set in The Legend of Zelda universe, and with SEGA AM2 since 2012's Dead or Alive 5, co-developing an Arcade version of the title, as well as on bringing characters from Virtua Fighter to Dead or Alive.

[14] Further restructuring at Koei Tecmo in 2016 resulted in Team Tachyon, the developers behind Quantum Theory as well as Rygar: The Battle of Argus being shut down.

[18] When first presented with the project by Koei, Team Ninja staff were skeptic about the game's concept, citing the western protagonist in Sengoku-era Japan, as well as various mechanics.

[26] As of 2022, Yosuke Hayashi had left Team Ninja to serve as the general manager of Koei Tecmo's entertainment division,[27] with Fumihiko Yasuda replacing him as president.

[31] Tomonobu Itagaki was promoted to Tecmo Executive Officer in June 2004, as well as to General Manager in 2006, alongside his position as the head of Team Ninja.

[32] On June 3, 2008, Itagaki announced that he would be leaving Tecmo and Team Ninja on July 1, 2008, citing difficulties with the company.

[33] Another lawsuit followed shortly after which was filed on 16 June by two plaintiffs on behalf of Tecmo's 300 employees for unpaid wages amounting to ¥8.3 million.

[27][28] Team Ninja's provocative style, originally coined by Itagaki,[3] while often having been praised, with Dead or Alive's Kasumi being regarded as a modern-day sex symbol,[37][38] with MTV UK labeling her as one of the sexiest characters in video games,[39] has been accused of objectifying women.

[40][41] In a 2012 Interview with Kotaku, Yosuke Hayashi said that Team Ninja was "very misinterpreted" outside of Japan, and that there's no derogatory intention in their creation process.

[41][43][44] Shuhei Yoshida, president of Sony Interactive Entertainment at the time, said in a statement in regard to Dead or Alive Xtreme 3 that Europe and North America have their cultural differences about how to depict women in video games and other media.

[45] In 2008, the German Rating Board USK refused classification for Ninja Gaiden II, banning the game for sale in Germany, due to the title's excessive violence.

[48] In 2011, Dead or Alive: Dimensions was banned in Sweden, due to the rating board determining that the characters appeared too young.

[50][51] In 2019, Team Ninja gained controversy, due to a livestream of Dead or Alive 6 at Evo Japan 2019 featuring gravure idols.

[52][53][54][55] Evo 2020 would be cancelled and Cuellar removed as CEO, due to a history of sexual abuse towards minors coming to light.