Coral Reef Conservation Amendments Act of 2006

Establishes as additional coral reef conservation project approval criteria that a project will: (1) minimize vessel impacts on coral reefs; and (2) promote and assist entities to work with local communities, and appropriate governmental and nongovernmental organizations, to support community-based planning and management initiatives for the protection of coral reef systems.

Authorizes the Administrator to undertake emergency response actions to prevent or minimize the destruction or loss of, or injury to, coral reefs or coral ecosystems from vessel impacts, derelict fishing gear, vessel anchors and anchor chains, or damage from unforeseen or disaster-related circumstances.

Authorizes, under the national program to conserve coral reefs and coral ecosystems, activities designed to minimize the likelihood of vessel impacts or other physical damage to coral reefs, including activities to identify certain at-risk coral reefs.

Authorizes the Administrator to make community-based planning grants to certain entities to work with local communities and appropriate federal and state entities to implement plans for increased protection of high priority coral reefs.

Authorizes the Administrator to: (1) maintain an inventory of all vessel grounding accidents involving coral reef resources; and (2) identify certain at-risk coral reefs that have a high incidence of vessel impacts, including appropriate measures to reduce such impacts.

Reauthorizes the Coral Reef Conservation Act of 2000 and authorizes appropriations through FY2012 for: (1) the coral reef conservation program; and (2) community-based planning grants.