"The truth is, Konami [had legal problems with] Russian composers who said we stole their music," Hibino told EGM, as related by Gamasutra. "They didn't, actually. But Konami was too sensitive about the situation and just decided not to use that music in the game."
The unnamed Russian composers apparently allege that the theme was stolen from Russian composer Georgy Sviridov's concerto "Pushkin's Garland" from 1979.
The Metal Gear Solid theme is credited to composer Tappi "TAPPY" Iwase, and first debuted with the PlayStation release of Metal Gear Solid in 1998.
Below the fold is a video of Metal Gear creator Hideo Kojima essentially getting "Das Punked" with the tune by a Russian magazine. Judge for yourself whether the Metal Gear theme is the result of plagiarism or coincidence.
I had wondered about this :(