The Department of Defense ordered General Electric and Rolls-Royce on Thursday to stop work on an alternate engine for the new F-35 joint strike fighter.

For the past three years, Defense Secretary Robert M. Gates has tried to halt spending on the second engine, but each time Congress has re-inserted funds so that about $3 billion has now been spent on the project.

In releasing notice of the order, the Pentagon said current spending of about $1 million per day “is a waste of taxpapyer money that can be used to fund higher departmental priorities and should be ended now.” The order lasts for 90 days, during which time Congress will have time to act on the matter.

Pratt & Whitney, which had a four-year head start on General Electric, is the main contractor for the F-35 engine and has so far received more than $6 billion to develop it. The competition has been intense because in the end more than 2,000 F-35s will be built under current plans.

In taking this step, the Defense Department noted that the House, which has always supported the second engine, last month changed direction and voted 233 to 198 to stop funding the program. Many freshman Republicans voted in the majority.

That measure has not passed Congress, but previously the Senate had voted against the second engine in the fiscal 2011 Defense Authorization Bill and Senate Democrats eliminated second engine funding in their most recent fiscal 2011 defense appropriations bill.

Since the Pentagon is operating under continuing resolutions that carry forward projects funded by the fiscal 2010 appropriations bill, money has continued to flow to the second engine.

Rep. Howard P. “Buck” McKeon (R-Calif.), chairman of the House Armed Services Committee and a supporter of the second engine, indicated Thursday he would fight to reinstate the money. He called the stop order an attempt to “preempt the congressional deliberation process by yanking funding after a single amendment vote.” Calling on Gates to “follow current law,” meaning the continuing resolution now in effect, McKeon said, “We will explore all legislative options available to us to maintain engine competition.”

General Electric spokesman Rick Kennedy said in a statement that the company will use its own money to continue the engine project during the 90-day period because “we feel so strongly about this issue, as do our Congressional supporters.”