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“It does not mean regulation,” Mrs. Jackson said. “I have said over and over, as has the president, that we do understand that there are costs to the economy of addressing global warming emissions and the best way to address them is through a gradual move to a market-based program like cap-and-trade.”

The cap-and-trade proposal would set an overall ceiling for greenhouse-gas emissions and allow businesses and other polluters to trade emission permits under the cap.

An EPA spokeswoman said Mrs. Jackson would consider the dissenting views from within the administration when drafting a final “endangerment finding.”

“As we do with any proposed rule, EPA takes these interagency comments under advisement,” said EPA spokeswoman Adora Andy.

In making the initial finding, EPA acted in accordance with a court order, which said the agency must determine whether carbon dioxide was dangerous enough to deserve regulation under the Clean Air Act.

The Obama administration has walked a fine line with the finding - playing down its potential for regulating carbon dioxide while supporters have heralded it as a backup plan should climate legislation fail. Mr. Obama’s team has consistently said EPA regulations would be a dull tool and prefers that Congress come up with a solution.

House lawmakers are weighing a plan to address climate change through the “cap-and-trade” system, but the proposal is facing early opposition in a House committee.

The memo was first reported by Dow Jones Newswire, and the intra-administration dispute could give opponents ammunition for a legal challenge to EPA’s finding.