The U.S. said Texas hasn't been doing enough to make sure companies don't treat major changes to their plants as minor ones.

The Environmental Protection Agency signaled Tuesday that it is serious about demanding changes in the way Texas issues air pollution permits to major industries.

Federal officials said they intend to disapprove three Texas permitting programs that deal with emissions from factories, power plants, refineries and other industrial plants. The proposal, which is open to public comment for 60 days, will trigger months of negotiations with the Texas Commission on Environmental Quality.

The EPA move may be the opening of a new, less-cozy relationship between the federal agency and the state, which handles several federal environmental laws on behalf of the EPA. The EPA delegates power to the states for many federal environmental functions, but if things go poorly, the EPA can take that power away.

EPA Administrator Lisa Jackson said during a visit to Dallas on June 12 that she had problems with the way Texas was handling air pollution permits. She singled out openness of the process to the public as a concern.

In targeting three Texas permitting programs on Tuesday, the EPA said the TCEQ hasn’t been doing enough to make sure companies don’t treat major changes to their plants, which trigger much more intense regulatory scrutiny, as minor ones that get less attention.

That problem, the EPA said, has made it difficult for the public to track industrial permits and take part in regulatory decisions. Larry Starfield, the EPA’s acting regional administrator in Dallas, said in a statement that some aspects of Texas’ programs don’t meet the requirements of the federal Clean Air Act.

“Texas’ air permitting program should be transparent and understandable to the communities we serve, protective of air quality, and establish clear and consistent requirements,” Starfield said. “These notices make clear our view that significant changes are necessary for compliance with the Clean Air Act.”

The TCEQ said its permits comply with federal law. Commission executive director Mark Vickery said in a statement that the programs the EPA rejected “have proven to be extremely successful in the reduction of air emissions in Texas.”

He said the TCEQ hopes the EPA will look at the programs’ achievements “and will continue to build on those successes. Our environment is too important to be a casualty of the bureaucratic process.”

The EPA rejected Texas’ flexible permits program, which streamlines reviews of complex facilities, and two systems that govern new plants or changes to existing ones. All three programs raised similar concerns about inadequate review of emissions sources, the EPA said.

Most plants with flexible permits are in the Gulf Coast petrochemical corridor near Houston, Port Arthur, Beaumont or Corpus Christi, although 12 are in the Dallas-Fort Worth area, according to the EPA. They include Forbo Adhesives, Dal-Tile and Motiva’s petroleum terminal, all in Dallas, General Aluminum in Carrollton and Sherwin-Williams’ paint factory in Garland.

The effect of the EPA announcement on any current permit holder will not be known until Texas and the EPA negotiate changes to Texas’ system. That could take months or longer.