Square Enix Holdings: ¥21,680,000 (US$272,988)
Sony: ¥9,230,000 ($116,189)
Nintendo: ¥9,140,000 ($115,032)
Sega Sammy: ¥8,220,000 ($103,486)
Konami: ¥6,780,000 ($85,371)
Namco Bandai: ¥6,400,000 ($80,577)
Tecmo Koei: ¥6,150,000 ($77,418)
Capcom: ¥5,710,000 ($71,891)
A couple things to keep in mind: The strong yen makes the salaries appear much larger in US dollars. Also, this doesn't necessarily mean your typical Square Enix employee is earning $200k. Rather, it probably means there is a layer of upper and mid-management with very high salaries.
As reader Brady pointed out, Square Enix is divided into development and its holding company. So Square Enix Holdings has only 18 employees—meaning that these are not game developers slaving away on new titles, but rather, people in management. It's odd that Nensyu Labo would include them with "regular" game companies as it skews the rankings.
The ranking also showed which game developers brought up the rear of the pack—namely folks like Nippon Ichi Software (3,700,000 or $46,512) and Tose (¥3,500,000 or $43,995). Give those people raises!