WASHINGTON — Defense Secretary Lloyd J. Austin III has sent to leaders of the Armed Services panels a 15-page letter detailing his serious worries about several dozen pending provisions in the House or Senate NDAAs.

Some of these are “topics of significant concern,” Austin wrote in the Sept. 26 letter, obtained by CQ Roll Call. “lf left unaddressed, certain provisions in the House-passed or Senate-proposed bills will substantially impact the Department’s ability to accomplish our strategic goals.”

House and Senate negotiators have begun reconciling the House-passed fiscal 2025 NDAA, or National Defense Authorization Act, with the Senate Armed Services Committee’s version and hope to clear a bicameral measure later this year.

Austin’s new missive is this year’s version of an annual Pentagon communication, known as the “heartburn letter.” In it, the department tells the authorization committees of provisions in the House or Senate NDAA that are causing the department worry as lawmakers meet to write a final version of the measure.

The new letter reiterates some Pentagon concerns that were previously known — for example, about provisions in the House GOP-authored bill to limit what the U.S. military can do on “culture war” matters such as transgender health care and diversity promotion.

But the document also reveals Defense Department concerns about numerous other provisions that are less well-known. These include a number of NDAA proposals to prescribe or proscribe weapons or military organizations, as well as disclosure of several cost estimates and projections of budgetary implications.

Austin thanked the defense authorizers for major investments in U.S. defense programs.

“Nevertheless,” he added, “the respective FY 2025 House-passed and Senate-proposed NDAA bills include certain provisions of significant concern to the Department.”

In the document, Austin reiterated the department’s opposition to procuring a second Virginia-class attack submarine in fiscal 2025. He conveyed officials’ concern that U.S. sub manufacturers lack the workforce and capacity to build two attack subs this fiscal year and deliver them on what he called “a reasonable schedule.”

The secretary argued that being required to build the second sub would force a $400 million cut to the Navy’s developmental “next generation fighter” program, making it “unexecutable and degrading the Navy’s ability to field next generation aircraft capabilities required in the 2033 to 2037 timeframe.”

In addition, Austin said the department “strongly objects” to the House’s proposal to increase pay for junior enlisted military personnel by nearly 20%, saying it is excessive and would unacceptably narrow the difference between junior and senior pay rates.

The House’s proposed pay changes “would cost over $3.3 billion in FY 2025 and a total of more than $21.9 billion from FYs 2025 to 2029,” he wrote.

Austin also pushed back against proposed directives on what the Pentagon should buy or maintain in its inventories.

He objected, for example, to the House bill’s requirement that the Pentagon build a third missile-defense site on the East Coast to protect against a ballistic missile attack. He said it is not necessary and would cost $5 billion to construct.

He also expressed concern about mandates in one or both bills to restrict the department’s planned reductions to certain types of aircraft and other assets or to limit Pentagon’s options on force structure and basing decisions.

He also criticized a House provision that would block a planned 3,000-soldier reduction to Army special forces end strength.

Similarly, Austin assailed the Senate bill’s proposed restrictions on cutting U.S. forces in Syria and on closing the U.S. military-run prison at Guantanamo Bay, Cuba, or moving detainees from there to U.S. prisons.

Austin also opposed a Senate mandate to reestablish a chief management officer position and another to set up a new assistant secretary for nuclear deterrence policy and programs.

He took aim, too, at a House proposal to cut the department’s discretionary budget by 0.5% if the Pentagon does not produce an “unqualified audit opinion” on its financial books by 2029.

Last November, the Pentagon released for the sixth consecutive fiscal year a department-wide audit with a disclaimer of opinion — meaning the financial statements were once again not, in the view of independent auditors, reliable enough for them to reach conclusions.

Austin also opposed inclusion of 23 military construction projects that would only be partly funded and as such, he said, would create an “unfunded obligation” of $2.4 billion in future budgets. And he hit proposed reductions to fully funded projects in the president’s request that would pay for lawmakers’ preferred work.

The House-approved so-called culture war provisions that drew Austin’s opposition in the letter would:

—Cut back on programs to promote “diversity, equity and inclusion.”

—Bar the military’s health care system from covering gender transition.

—Prohibit spending on certain initiatives to address military “resilience and survivability” in the face of climate change.

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