The unique way Texas regulates air pollution from refineries, chemical plants and other major industries is no more — for now.

The EPA said Tuesday all 136 industrial plants with state-issued permits that do not meet federal Clean Air Act requirements have agreed to apply for new ones.

The announcement comes one year after the federal agency rejected Texas' use of so-called flexible permits. But the dispute is not over, because state officials and at least 10 industry groups are challenging the EPA's actions in federal court.

Gov. Rick Perry and other Texas officials have said the EPA was threatening jobs by forcing permit changes at the facilities, including some of the largest refineries in the nation.

Al Armendariz, the EPA's regional administrator for Texas, said the companies are converting their permits without any job losses.

"We're really happy," he said. "All the permit holders have agreed to get federally compliant permits, and we've done it without any economic disruption."

Not everyone is happy.

Debbie Hastings, a vice president for the Texas Oil and Gas Association, said the group will push forward with its lawsuit against the EPA over flex permits, asserting that the agency had no legal basis to reject them. Some companies, she said, agreed to seek revised permits "to establish some semblance of stability and certainty sooner rather than later."

The Texas Commission on Environmental Quality also expressed "regret" that some businesses were forced into an "unnecessary permitting process by the EPA, even though existing permits were legal and protective of the environment."

What's more, the TCEQ, which issues permits for the EPA, said that companies made no significant changes to their permits as a result of the federal agency's actions.

The permits in question require refineries, chemical plants and other facilities to meet an overall emissions cap but allows them to choose how to do so. Federal rules, however, require plants to limit emissions of certain pollutants from each source within a facility.

The single overall cap, the EPA argues, makes the Texas permits unenforceable and allows plants to emit more than similar facilities in other states. But Texas officials say the system cuts red tape and pollution without violating federal law.

Armendariz said the move by industry to more detailed permits provides them with regulatory certainty and will lead to cleaner air.

"The issue is settled in respect that flexible permits will not be issued in Texas," Armendariz said.

While Texas officials and industry continue to defend flexible permits, "the real proof is in the pudding," said Ilan Levin, an attorney for the Environmental Integrity Project. "It shows that Texas industry understands that these flexible permits are too risky for them."

matthew.tresaugue@chron.com