The title will feature a new story and be set in 1935 Europe, the same period as the first game for PS3, according to Famitsu (via Andriasang).
It will include a new cast of characters that are designated numbers rather than names due to incidents that have happened to them in the past.
The mission-based structure of the second game will be dropped in favour of battles to advance through the story, and will add a new command interface and more varied map design.
Wireless play will also be omitted from the title, as producer Shinji Motoyama said that he wanted to focus on the story and that resources have been used to improve gameplay systems elsewhere.
Motoyama added that while players wanted a PS3 sequel, it would require new ideas beyond standard gameplay updates and the firm plans to reserve them for an entirely different project.
News of the title was leaked earlier this week. SEGA is expected to formally announce the game during a panel at TGS tomorrow.
It will be released in Japan early next year.