Don’t hold your breath waiting for Congress to follow up on a recommendation from Director of National Intelligence James Clapper to separate the budget for the National Intelligence Program — which funds the CIA and other intelligence agencies — from the Defense Department budget.

Intelligence spending has always been hidden in the Defense Department. Clapper’s plan would, at a minimum, reduce the defense budget and provide a measure of transparency into the country’s real defense costs. The plan could also strengthen Clapper’s hand as director of national intelligence.

While he effectively has statutory authority over all intelligence spending, he has somewhat less control over spending in the Defense Department’s Military Intelligence Program, and even over spending in the Pentagon’s intelligence collection agencies, such as the National Security Agency, that do work for the National Intelligence Program.

But with Clapper’s notion hanging out there, the House Appropriations Committee recently made its sentiments known by adding into the current fiscal 2012 Defense Appropriations bill legislative language aimed at prohibiting the budget separation from taking place.

Steven Aftergood, who first publicly focused on the House committee’s action in his Secrecy News blog, said the recent committee action ends an opportunity to “increase the transparency and the integrity of the budget process.”

Way back in 2004, the Sept. 11 commission recommended changes in how congressional committees dealt with the intelligence community. Although there have been some baby steps toward its recommendations, there have been few if any significant reforms. And the House committee’s recent actions illustrate how difficult it has been to make any changes.

All of the provisions in the Defense Department budget that involve the National Security Program or the Military Intelligence Program go through the House and Senate intelligence committees for authorization. All of the provisions involving Pentagon agencies, whether related to the National Intelligence Programs or not, go through the House and Senate Armed Services committees and the House and Senate Appropriations committees.

In October, the budget for the Military Intelligence Program was disclosed for the first time, along with the budget for the National Intelligence Program. For fiscal 2010, Congress authorized $27 billion for the former and $53 billion for the latter.

Of course we will probably have to wait until after fiscal 2011 ends in October to find out how much the intelligence community spent this year. Meanwhile, the figure for both the National Intelligence Program and the Military Intelligence Program for the next year is buried somewhere deep in the Pentagon’s fiscal 2012 budget.

The Senate Appropriations defense subcommittee is taking testimony about both programs on Tuesday, but it it doing so behind closed doors. Clapper will appear along with Michael G. Vickers, the undersecretary of defense for intelligence.