The library project emerged when Murakami offered to donate his growing collection of materials.
Murakami grateful for nomination, but says he wants to 'concentrate on writing, away from media attention'.
The writer, who spends much of his time in the United States, has a cult following for his sometimes surreal works peppered with references to pop culture, which have been translated into some 40 languages.
Murakami said the Aum-related cases did not come to a close with the latest executions.
More than 2,100 residents had signed an online petition as of Thursday against the move, which requires Murakami's "Killing Commendatore" to be sealed in wrappers with warning notices.