House defense appropriators want to kill the F-35 Joint Strike Fighter’s alternate engine and trim the Pentagon’s requested levels of procurement and research funding in the budget bill they plan to approve today.

The House Appropriations Defense subcommittee (HAC-D) released a draft of its fiscal year 2012 defense appropriations bill yesterday, before it is set to mark up the bill in a closed hearing today. The subcommittee’s plan calls for cutting President Barack Obama’s $539.5 billion defense budget request by $9 billion, down to $530.5 billion. The legislation would give a slight boost to Obama’s separate war funding proposal, raising it from the $117.8 billion requested to $118.6 billion.

The legislation notably does not fund the F-35’s second engine, developed by General Electric [GE] and Rolls-Royce.

A House Republican aide said the lack of funding for the controversial engine is “consistent with the position of the House,” which voted in April to kill FY ’11 funding for it.

Given “the current fiscal crisis, it is essential to find savings wherever possible to help rein in the nation’s historic deficits and debt,” the aide said.

The Pentagon terminated the second-engine program in April after Congress, for the first time, agreed to stop funding for it. General Electric and Rolls-Royce, though, have pledge to spend their own money to continue developing the engine in FY ’12, which starts Oct. 1.

The policy-setting defense authorization bill the House passed last Thursday includes language intended to help the companies with that second-engine plan. The White House, though, said Obama would veto the authorization legislation if the final version “includes funding or a legislative direction to continue an extra engine program.”

Congress in recent years kept the second-engine program alive despite the Pentagon’s attempts to cancel it.

The HAC-D, which writes the budget-setting defense appropriations legislation, is not as supportive of the alternate engine as is the House Armed Services Committee, which crafted the authorization bill. Opponents argue the engine, an alternate to the main one made by Pratt Whitney [UTX], is a waste of money, while supporters believe competition is needed for the engine that will power the multi-service, multi-nation fighter jets.

The draft HAC-D bill is causing some concern among advocates of hearty weapons-system spending because it cuts Obama’s request for procurement, from $114.4 billion down to $107.6 billion, and research and development, from $75.3 billion to $73 billion.

“The draft is a minor negative for defense stocks” because of the procurement and research funding cuts, analyst Byron Callan, director of Capital Alpha Partners LLC in Washington, wrote in a note yesterday. Still, he noted the defense budget “has a long route to travel before completion.”

The HAC-D’s proposed procurement cuts would reduce the administration’s request for Navy aircraft and shipbuilding. Yet not all services would see procurement reductions, and the Marine Corps procurement request is increased by $100 million in the HAC-D’s draft bill.

HAC-D Chairman C.W. “Bill” Young (R-Fla.) said yesterday his panel’s draft bill would give the Pentagon “the resources it needs to continue our overseas commitments.”

“It also allows us to continue to modernize and maintain readiness at the levels needed for our military to preserve its standing as the most capable and superior armed forces in the world,” he said.

HAC-D Ranking Member Norm Dicks (D-Wash.) said yesterday that House Republicans’ “approach to the defense budget has been reasonable.” The draft bill, he said, “makes the necessary investments needed in research and development, and equipment acquisition.”

The HAC-D legislation includes: $15.1 billion for building 10 Navy ships; $5.9 billion for 32 F-35s (19 for the Air Force, seven for the Navy, and six for the Marine Corps); $2.8 billion for 116 H-60 Black Hawk helicopters; $1.4 billion for 47 CH-47 Chinook helicopters; $1.1 billion for 11 C-130J aircraft; and $699 million for 48 MQ-9 Reaper UAVs. It calls for granting the Pentagon its request for the Air Force tanker aircraft, P8-A Poseidon, Broad Area Maritime Surveillance unmanned aerial vehicle, Navy Combat Air Vehicle, and CH-53K helicopter.

Cuts to the Pentagon’s proposal in the legislation include a $435 million reduction to the Advanced Medium-Range Air-to-Air Missile (AMRAAM) and a $524 million cut for the Enhanced Medium Altitude Reconnaissance and Surveillance System (EMAARS) efforts.

The full HAC is slated to mark up the defense bill on June 14.