Surety Bond Improvement Act of 2006 - Amends the Small Business Investment Act of 1958 to: (1) authorize the Administrator of the Small Business Administration (SBA) to guarantee any surety against loss from a small business principal's breach of bond on any total work or contract amount that does not exceed $3 million (currently, $2 million); (2) allow the Administrator to authorize a surety that issues, monitors, or services such bonds to use rates approved by the insurance commissioner in the state in which the contract will be performed; and (3) prohibit the Administrator from refusing to make payment on a surety guarantee based on facts, circumstances, or defects that the Administrator should reasonably have identified during the guarantee process.

Requires the Administrator to notify the congressional small business committees regarding a proposed change in fees charged to guarantee surety bonds.

Expresses the sense of Congress that the surety bond guarantee program is not required to be self-funding and, therefore, may at times operate at a loss.