In 1988, Toho released on VHS Toho Unused Special Effects, which showcased many deleted clips, edited back into the film scene or in comparison to their final version. In the case of Mothra vs. Godzilla, there are a couple of scenes. The one discussed here is an extended opening. Instead of a ship destroying what was seen as a coast line resort, we have a hurricane wave come up and crashing into a giant hedge which acts like an arc. Then the scene fades into an extended shot of the water pumps, with the scene beginning even further behind the pumps which allows the audience to see more of the devastation.

There was additional footage filmed for Godzilla's initial appearance in the movie than was shown in the final cut of the 1964 movie. As shown in the picture, there are some full body shots of Godzilla after emerging out of the dirt that were filmed for this sequence, but never used.

For the movie's first battle sequence, a lot of unused footage was filmed and cut for various reasons. To begin with, instead of Godzilla dazing at the giant egg before Mothra starts attacking, we get a shot of Godzilla looking up via a puppet to see the approaching Mothra. Later, the same puppet and the Mothra marionette fight each other in front of a blurry background piece. The rest of the battle goes on as in the film until Godzilla walks up to Mothra after burning her wing. An alternate angle of Godzilla approaching Mothra is used, and after the creature takes off to land on her egg we get a shot of Godzilla roaring from a low point of view.

Additional footage of Godzilla's final battle in the movie was lensed but never used in the final print. About seven seconds of Mothra spraying Godzilla was cut. An alternate version of Godzilla falling into the water was also filmed, with the sequence being shot from above and along with it clearly showing the use of the Godzilla suit from King Kong vs. Godzilla (1962).