A source told retail publication MCV that the title will miss its expected summer release date but will be available in time for Christmas.
It will launch alongside other Konami titles Silent Hill: Downpour and PES 2012 in the third quarter of this calendar year.
First released in 2004 on PlayStation 2, the third game in the Metal Gear Solid series is a prequel featuring Big Boss as a playable character.
The 3DS version will include higher resolution textures, support for 3D visuals and other platform specific additions.
> Read our hands-on with the Snake Eater 3DS demo