Defense Secretary Ash Carter sent a warning to Congress on Thursday that the president would veto its pending defense policy bill if major changes aren't made.

"If a bill is presented to the President in the current form of either version of the NDAA, I will join with the President's other senior advisors in recommending that he veto the legislation," Carter said in letters to Senate and House Armed Services Committee chairs Sen. John McCain John Sidney McCainMomentum growing among Republicans for Supreme Court vote before Election Day McConnell urges GOP senators to 'keep your powder dry' on Supreme Court vacancy McSally says current Senate should vote on Trump nominee MORE (R-Ariz.) and Rep. Mac Thornberry (R-Texas).

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Some of its provisions amount to "excessive micromanagement," he charged.

While the Obama White House has threatened vetoes on the National Defense Authorization Act every year, making this objection letter public is a rare, if not unprecedented, move by the administration.

It comes a day after House and Senate members formally began a conference process where they will merge their respective bills together for final passage.

Carter said his "most urgent concern" was the House bill's redirection of $18 billion from the Pentagon's war fighting fund into its base budget. The money would pay for retaining troops the Pentagon had planned to cut, a troop pay raise, and equipment requested by the services but not included in the administration's defense budget request.

House Republicans have argued that the incoming administration would make up for that shortfall with a war supplemental when war funds run out in April 2017, as the Obama administration did when it entered office in 2009.

Carter said his next "serious concern" was the bills' "intrusive provisions" to reform the Pentagon's structure.

"For example, 131 acquisition policy provisions, 120 military personnel policy provisions, and 69 health care provisions in the House and Senate bills will require extensive implementation efforts by headquarters elements in the Office of the Secretary of Defense and the military services," he said.

One proposal would would split an office in charge of weapons buying, technology and logistics into two. Another would create a new Assistant Secretary that Carter said would create "bureaucratic overlap" with the Principal Advisors for Space and Cyber, two newly created positions.

Another proposal would cut down the number of generals, admirals and civilian equivalents by 25 percent, which Carter said "will damage the enterprise's ability to oversee global operations, support the warfighter and military families, and ensure the best stewardship of taxpayer dollars."

At the same time, the provisions would necessitate increased headquarters staff, Carter said.

Carter said his third big concern is Congress' continued blockage of the Pentagon's cost-saving proposals, such as getting rid of excess military bases in another round of base closures, and retaining more military equipment than the Pentagon wants, like extra Littoral Combat Ships.

He also lists a number of other reform proposals he disagrees with, such as with military health care reform, housing allowances, and provisions he said appear to be ideologically driven.

"Congress needs to join the department in making the tough budget choices that are necessary in this environment," Pentagon press secretary Peter Cook said during a briefing Wednesday after he announced the letter.

"It's important to note that Secretary Carter's message to Congress reiterates that if legislation in the current form of either the House or the Senate bill is presented to the president, the secretary will recommend a veto of that legislation."

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