The Japanese must be very forgiving people, especially after that whole demolishing a city thing. 

The government of Japan has obviously made a very wise decision by granting citizenship to a city destroying, skyscraper tall radioactive lizard. The city of Shinjuku has granted him citizenship and he can now call the city his permanent home. The paperwork even has April 9th, 1954 as his date of birth. That is the release year of the first Godzilla film. The previous visits to the Shinjuku Ward lists the title and release years for all of the current Godzilla films.

The ceremonial certificate also gives a reason for special residency:

Promoting the entertainment of and watching over the Kabuki-cho neighbourhood and drawing visitors from around the globe in the form of the Godzilla head built atop the Shinjuku Toho Building.

The city also announced Godzilla as their "'tourism ambassador' to represent the country on the international stage." Sadly, as long as people in New York remember his trip there, not to mention the actual movie starring Mathew Broderick, he won't be back in the U.S. anytime soon.