Clean Energy Partnerships Act of 2009

Clean Energy Partnerships Act of 2009 - Requires the Secretary of Agriculture and the Administrator of the Environmental Protection Agency (EPA) to establish: (1) a program to govern the creation of credits from emission reductions from uncapped domestic sources and sinks; (2) the Greenhouse Gas Emission Reduction and Sequestration Advisory Committee to provide scientific and technical advice on the establishment and implementation of such offset program; and (3) a carbon conservation program to provide incentives to landowners or grazing contractor holders to implement projects that reduce greenhouse gas (GHG) emissions or sequester or permanently store carbon through conservation easements, sequestration contracts, and timber harvest or grazing contracts with the Department of Agriculture or the Department of the Interior.

Requires the Administrator to establish a registry to record approved credits issued under such offset program. Requires each appropriate official to: (1) establish and maintain a list of types of offset projects eligible to generate offset credits under the program; and (2) prescribe regulations to ensure the emission reduction integrity of the offset projects.

Authorizes the Administrator to issue offset credits for emissions reduced by specified international projects that reduce deforestation.

Provides that a person is not required to hold allowances or credits for emissions resulting from the use of gas as an energy source if the gas is derived from an approved domestic methane offset project.

Establishes: (1) the Carbon Conservation Fund for the carbon conservation program; and (2) the Rural Clean Energy Resources Fund to provide assistance for the development of biofuel and bioenergy, including by supporting the Rural Energy for America Program and implementing a research and demonstration program that includes approaches to sequestering carbon through agricultural, grazing, and forestry practices and reducing methane and nitrous oxide emissions associated with agricultural production.