The $16.5 billion NASA budget the U.S. Congress approved and sent to the White House Nov. 16 largely funds the U.S. space agency’s new exploration priorities but leaves unaddressed NASA’s main problem in the years ahead.

The space shuttle program is under funded by $5 billion or more over the next five years, a revelation that has only come to light since NASA sent its 2006 budget request to Congress in February.

So while Congress fully funded NASA’s $4.5 billion request for the space shuttle program for the year ahead, it was silent about a budget problem that threatens to bog down the agency’s space exploration agenda.

The predicted gap between the amount of money NASA now believes it will need to properly fund the shuttle program until it is phased out in 2010 and what had been forecast previously, is the result of past budget planning that was predicated on the assumption that a dramatic decline in shuttle spending would be possible as the program winds to a close.

With such a decline now considered unlikely, finding the money to close the predicted shortfall is the central dilemma NASA and the White House will be dealing with as they work to finalize the space agency’s 2007 budget request.

With lawmakers in both major U.S. political parties in Congress drawing a line against further reductions in the budgets for NASA’s science and aeronautics programs , the shuttle program’s funding shortfall will almost certainly be felt the most by NASA’s Exploration Systems Mission Directorate.

Exploration Systems already has made deep cuts to its life science research and technology development accounts in order to put more money into its primary efforts: fielding a Crew Exploration Vehicle and Crew Launch Vehicle by 2012, two years sooner than originally planned. Those two efforts, known collectively as Project Constellation, will get $1.7 billion of NASA’s budget in the year ahead.

NASA sent Congress a detailed list in late October of the Exploration Systems research and technology projects it is canceling in order to plow the savings into Project Constellation.

In the conference report accompanying the $61.8 billion spending bill that funds NASA and numerous other federal agencies, including the Commerce, State and Justice departments, lawmakers said nothing about shuttle’s budget shortfall but rather expressed concern about “the impact the accelerated schedules for [development of the Crew Exploration Vehicle and its solid-rocket booster-based launcher] will have within the agency.”

Overall, the budget bill Congress sent to the White House to be signed into law provides $1 million more than NASA requested and $260.3 million more than NASA received for 2005.

But tucked into the bill are some 185 special projects lawmakers added that will cost NASA $270 million in the year ahead.

Lawmakers also made plain where they stand on science and aeronautics spending, directing NASA to spend $200 million more than it had planned to spend next year on aeronautics research and various science efforts.

Congress denied NASA’s plan to cut aeronautics spending, adding $60 million to keep that account on par with what it received for 2005.

Lawmakers also directed NASA to spend $50 million more than it budgeted to prepare for a Hubble Space Telescope servicing mission it intends to fly if the next space shuttle mission, slated for the summer, goes well.

Glory, a greenhouse gas-measuring satellite mission that lawmakers saved from cancellation earlier this year, is in for a $30 million increase in the 2006 budget. Living with a Star, a multiple spacecraft campaign to study the interaction between the Earth and the S un, received a $5 million increase from Congress, bringing its total budget up to $239 million for the year ahead.

Congress also approved NASA’s plan to spend more on competitively selected Discovery-class missions, although not by as much as NASA had requested. NASA had planned to raise the cost cap on Discovery missions to $450 million, a $100 million increase over the cap that has been in place for at least three years. NASA said the increase is necessary to cover increased launch costs and other inflationary pressures. Congress approved raising the cap to $425 million.

Although Congress provided no additional money for the James Webb Space Telescope, a program wrestling with a $1 billion cost overrun, it directed NASA to spend the full $371.6 million it requested for the program. The move limits NASA’s flexibility as it finalizes a new plan for the $4.5 billion telescope that includes delaying the launch two years to 2013.

Part of NASA’s plan for dealing with the Webb overrun involves further delaying the Space Interferometry Mission, but Congress guarded against near-term cuts to that program by adding $10 million to its 2006 budget.

NASA Administrator Mike Griffin issued a written statement after the budget achieved final passage, thanking the House and Senate “for endorsing and funding, for the second straight year, our activities to implement America’s Vision for Space Exploration.”

Griffin said the budget Congress approved provides funding that will enable NASA to continue to operate the space shuttle, resume assembly of the international space station, begin development of the Crew Exploration Vehicle and its launcher and “support key science and aeronautics programs vital to our nation.”

Griffin’s statement makes only indirect reference to the budget challenges that lie ahead for NASA. “We will work to ensure the president’s exploration priorities are maintained as we move forward in setting program and investment priorities,” Griffin’s statement concludes.

Brian Berger is editor in chief of SpaceNews.com and the SpaceNews magazine. He joined SpaceNews.com in 1998, spending his first decade with the publication covering NASA. His reporting on the 2003 Space Shuttle Columbia accident was...