Updated 5/18/16 with response from a Senate Armed Services Committee staffer.

WASHINGTON — Defense secretary Ash Carter today pushed back two major changes for the Pentagon put forth by the Hill, including stating he would recommend a veto by President Barack Obama if certain language from makes it through Congress.

Speaking at the annual Sea-Air-Space conference outside of Washington, Carter focused on what he called "unhelpful micromanagement" from the Hill, whether it be over the Senate's plan to eliminate the undersecretary of defense for acquisition, technology and logistics (AT&L), the House's plan to end wartime contingency funding in April, or the refusal to allow the Pentagon to shut down installations round the country.

"I would respectfully suggest that the informed expert judgment of the civilian and military leadership at the Department of Defense which is embodied in our budget proposal should receive greater support and be subject to less micromanagement," Carter said.

Carter took roughly a fifth of his speech to defend the AT&L position, currently held by Frank Kendall and previously a spot Carter himself held.

Language in the Senate Armed Services Committee's version of the nation's defense bill, released late last week, eliminate the AT&L spot and hands its duties to a new undersecretary of defense for research and engineering, or USD(R&E), and the renamed undersecretary of management and support, or USD(M&S).

Senate staffers have defended the plan by pointing out it resembles a structure that was in place under the technology-focused tenure of Secretary of Defense Harold Brown. Carter acknowledged that, noting that he worked under Brown and then-undersecretary for research and engineering Bill Perry.

But, he warned, "separating research and engineering from manufacturing could introduce problems in the transition from the former to the latter, which is a frequent stumbling block for programs." As an example, the secretary pointed to the challenges that faced the F-35 joint strike fighter program as it moved into a low-rate production program – although it should be noted those issues cropped up under the existing AT&L model.

"Procurement and sustainment are tightly coupled to technology, engineering and development, and represent about 90% of the cost of most programs," Carter said. "Separating these functions makes no sense, as procurement and sustainment costs are controlled by decisions made during development. This proposal could also derail the success we've had lowering our contract cost growth on the most high risk contracts to a 35 year low."

Hours after Carter's comment, a staffer for the Senate Armed Services Committee shot back at Carter, telling Defense News that the secretary was "wrong" in his analysis.

"In reforming AT&L, the SASC does not split oversight of development and manufacturing. The new undersecretary for research and engineering would set defense-wide acquisition and industrial base policy and oversee the development and production of weapons and national security systems," the staffer said. "Much of this work would be done by a new assistant secretary for acquisition policy and oversight, which would report to the undersecretary and enable that leader to prioritize technological innovation. What would shift to the new undersecretary for management and support is oversight of purchases of goods and services that are not national security systems and line management of defense agencies that perform these and other core business functions."

Carter did offer a hand to the Hill, saying he would like to work with the committees on this issue and others, but warned that "an overly prescriptive approach risks unhelpful micromanagement, with a high potential for negative second and third order effects."

The secretary also warned that he would recommend a veto of the House language, following up on a White House memo threatening the same.

The House Armed Services Committee's plan diverts $18 billion in wartime funds toward base budget programs and skirt statutory budget caps. More offensively to Carter, the bill would cut off wartime funding on April 30, 2017, a gambit to force the next president to make a supplemental request to Congress. Carter has previously stated concerns over that provision.

"If a final version of the NDAA reaches the President this year includes a raid on war funding that risks stability and gambles with war funding, jeopardizes readiness, and rejects key judgments of the Department, I will be compelled to recommend that he veto the bill," Carter said. "I am hopeful, however, that we can work with Congress to achieve a better solution. Our warfighters deserve nothing less."

Twitter: @AaronMehta