Last fall, EPA announced proposals to disapprove three sets of Texas air pollution rule changes that don't comply with the Clean Air Act. Specifically, EPA has taken issue with the state's flexible permitting process, its definition of qualified facilities, and aspects of its New Source Review (NSR) program. Despite pronouncements of EPA/State cooperation, EPA has begun filing objections to some TCEQ-issued operating permits. These include permits issued to operating units at Exxon Mobil's Beaumont refinery, ConocoPhillips' Sweeny refinery and Dow Chemical facilities. In a move that the Texas officials have described as a blatant power grab, EPA stripped the state of jurisdiction over one of its biggest air permits — the Flint Hills Resources' East Corpus Christi refinery — barring Texas from issuing an operating permit to the refinery. EPA regional administrator, Al Armendariz, proclaimed that Texas must inform him by July 1 whether it can "can issue permits that are consistent with federal requirements, and if they can't, then we will." According to agency personnel, EPA plans to block dozens of other permits and potentially take back the power it delegated to Texas to issue air permits by June 30.

In a press release, Texas Gov. Rick Perry called EPA's aggressive action "baffling" given that since the Clinton administration approved the program in 1994, and since then "EPA's unelected bureaucrats haven't ruled on it once, yet, with the arrival of a new administration in Washington, they have put a bull's-eye on the backs of hardworking Texans." He complained that "[a]n increasingly activist EPA is ignoring the 22 percent reduction in ozone and 46 percent decrease in NOX emissions that Texas has achieved since 2000." Finally, he stated that "On behalf of those Texans whose jobs are threatened by this latest overreach, and in defense of not only our clean air program but also our rights under the 10th Amendment, I am calling upon President Obama to rein in the EPA and instruct them to study our successful approach for recommended use elsewhere."

In a TCEQ press release, Commissioners Buddy Garcia and Carlos Rubenstein challenged EPA's commitment to federal/state partnership. Garcia complained that "after failing to act on our rules for some 15 years — [EPA] has decided that instead of working with us they would just tell us how to run our state-delegated program, or else." According to Rubinstein "The time has come to end the double talk about our partnerships. Come to the table and negotiate in earnest."