The warning is the latest skirmish in an ongoing feud between California and the Trump administration. Last week, the EPA moved to roll back aspects of the Clean Air Act, which California has for years used to set its own emissions standards.
The federal government mandates how much pollution can be in the air. Lots of places in the country don't meet those standards. But no state has more problems than California, where 85 percent of the population — 34 million people — is breathing dirty air.
Federal law requires states with dirty air to come up with a plan on how to reduce pollution. Those plans must be approved by the EPA. The agency has a backlog of these plans awaiting approval, and California accounts for more than 130 of them, or about one-third of the total.
In a Tuesday letter sent to the California Air Resources Board, EPA Administrator Andrew Wheeler chastised California for its backlog of pending rules and regulations to reduce pollution in areas that do not meet federal air quality standards.
Wheeler blamed California for the backlog on Tuesday, saying most of the plans are "inactive" and have "fundamental issues related to approvability."
"California has failed to carry out its most basic responsibilities under the Clean Air Act, and as a result, millions of Californians live in areas that do not meet our nation's air quality standards," Wheeler said in a news release. "EPA stands ready to work with California to meet the Trump Administration's goal of clean, healthy air for all Americans, and we hope the state will work with us in good faith."
He asked the state to withdraw the plans and come up with new ones. If they don't, the government would punish the state by withholding federal road dollars – a process that could take up to 18 months.
Wheeler’s letter lists six California plans that are not in compliance. The letter also chastises Southern California's Coachella Valley for an inadequate plan addressing the 2008 ozone standard.
Much of California's smog problem comes from its 35 million registered cars and trucks, the most of any state. But the problem is also compounded in Southern California, home to two of the world's largest ports where much of the country's freight passes through and is carried away on diesel trucks and trains.
Only the federal government can regulate emissions from trains, planes, ships and heavy-duty trucks, according to Richard Corey, the executive officer of the California Air Resources Board.
"California and other states had to go to court, repeatedly, to get the EPA to implement the strict smog standards it claims to be worried about," he said.
The EPA says it plans to issue $40 million in grants to help areas around the country meet federal air quality standards, including several communities in California.
The Associated Press contributed to this report.