The Bush administration is right that a national policy to combat climate change is preferable to a state-by-state patchwork of rules. In the absence of a mandatory comprehensive federal policy to reduce greenhouse gases, however, states, Maine included, passed their own laws. That approach was undermined last month when the Environmental Protection Agency – for the first time – rejected a waiver request from California to enact vehicle emissions standards. Maine and 17 other states, representing nearly half the U.S. auto market, planned to adopt California’s standards.

The EPA’s rationale for denying the waiver is that Congress last month passed new fuel economy standards that will require passenger vehicles to average 35 miles per gallon by 2020. There are two major problems with relying on the new energy bill to supersede California’s standards.

The first is that improving fuel economy and reducing emissions are separate but related issues that can be addressed in different ways. Gas mileage standards are set by the Department of Transportation, with a focus on fuel savings and vehicle safety. The EPA, under the Clean Air Act, is required to protect public health and the environment. Further, the U.S. Supreme Court in April ruled that the EPA had the authority to regulate the emission of carbon dioxide and other greenhouse gases from cars because these emissions are a threat to human health and the environment. The agency had argued that carbon dioxide was not a pollutant so the federal government could not regulate it.

Setting fuel economy standards is one way to reduce greenhouse gas emissions because if a vehicle goes farther on a gallon of gas, it emits less. It is not the only way, however. Setting emissions standards, as California planned to do, allows for other means of reducing pollution, some of which may not even exist yet.

Which leads to the second problem – timing and scope. California’s law would require emissions reductions much sooner than the recently passed gas mileage standards. As originally passed, the California law would have required emissions reductions beginning next year. Moreover, according to Environmental Defense, the new mileage requirements will reduce greenhouse gas emissions by 418 million metric tons by 2020. If the EPA had granted California’s waiver the reduction would increase to 723 million metric tons.

In 1993, Maine joined with other New England states in adopting California’s Low Emission Vehicle program, and in 2005, the Maine Board of Environmental Protection approved rules to require emissions reductions among all cars on the road. California’s waiver needed to be granted for these rules to become effective.

Although required by law, the EPA has yet to provide scientific justification for denying California’s waiver request, the first denial in more than 40 requests from the state.

These shortcomings will no doubt get a lot of attention in court, where this debate is now headed. It should also get attention in Congress as lawmakers look for ways to reduce U.S. emissions.