Prevent Unfair Manipulation of Prices Act of 2009

Prevent Unfair Manipulation of Prices Act of 2009 - Amends the Commodity Exchange Act to cover: (1) energy transactions; and (2) coal, crude oil, gasoline, electricity (except financial transmission rights subject to the Federal Energy Regulatory Commission [FERC]), natural gas, and any substance used as a source of energy (other than an excluded commodity, a metal, or an agricultural commodity).

Extends the regulatory authority of the Commodities Futures Trading Commission (CFTC) to swap transactions in: (1) energy commodities; (2) energy transactions; and (3) energy transactions on foreign boards of trade.

Prohibits the CFTC from exempting energy transactions from futures trading regulation, unless certain notice and public comment requirements are observed.

Requires the CFTC to fix limits upon the aggregate number of energy transaction positions held by any person for each month across all markets subject to its jurisdiction.

Grants the CFTC exclusive authority to grant exemptions from position limits imposed upon energy transactions for bona fide hedging transactions and positions.

Requires the CFTC to disaggregate and publicize specified market data with respect to index traders and swap dealers and the identity of holders of positions in indexes in excess of position limits.

Empowers the CFTC to set limits to prevent excessive speculation in indexes.

Amends the Inspector General Act of 1978 with respect to the CFTC Inspector General.

Excludes from CFTC jurisdiction certain derivative transactions, swap transactions, and transactions in exempt commodities which settle and clear through a derivatives clearing organization registered with the CFTC. Prescribes requirements for alternatives to clearing through designated clearing organizations.

Specifies requirements for eligibility to purchase credit default swaps.

Requires the CFTC to charge and collect transaction fees from clearing organizations.

Amends the Natural Gas Act and the Natural Gas Policy Act of 1978 to: (1) grant the Federal Power Commission (FPC) and FERC cease and desist authority regarding violations; and (2) instruct the FPC to establish a refund effective date for an initiated proceeding.

Grants the CFTC oversight authority over carbon derivatives markets.