Hawaiian Sacred Sites Noise Reduction Act of 2006 - Amends the Wendell H. Ford Aviation Investment and Reform Act for the 21st Century to prohibit any commercial air tour operation from being conducted in airspace over: (1) the Kalaupapa National Historical Park; (2) the Kaloko-Honokohau National Historical Park; (2) the Pu`uhonua o Honaunau National Historical Park; or (4) the Pu`ukohola Heiau National Historic Site.