HOUSTON — The US Environmental Protection Agency yesterday officially overturned a 16-year-old Texas air permitting program it says violates the Clean Air Act, leaving some of the country’s largest refineries in a state of limbo.

The move comes after years of backdoor bickering, negotiations, and public arguments between the EPA and Texas. The argument recently escalated from a battle over environmental issues into a heated political dispute over states’ rights.

Governor Rick Perry has been using the disagreement to drive home his contention that President Obama’s administration is overreaching, and he said in a statement yesterday that “Texas will continue to fight this federal takeover of a successful state program.’’

The EPA’s decision, announced in a statement, will force some 125 refineries and petrochemical plants to invest millions of dollars to get new permits. Many of the plants may also have to invest in updates to comply with federal regulations.

The decision did not come as a surprise to Texas or the industries. Al Armendariz, EPA regional director, has said for months he would disapprove the permits if Texas did not comply with the Clean Air Act.

Bryan Shaw, chairman of the Texas Commission on Environmental Quality, insisted yesterday that the state’s permitting program complies with the Clean Air Act and has improved air quality in Texas. However, in an effort to satisfy the EPA’s concerns, Shaw said, the commission recently changed the rules but apparently the EPA “did not take them into consideration.’’

Texas can challenge the ruling in court.

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