WASHINGTON — The U.S. Missile Defense Agency (MDA) in 2009 made progress in testing and fielding systems, but backtracked in the areas of transparency and accountability, a congressional watchdog agency found.

Recent organizational and programmatic changes at the MDA have not been accompanied by needed improvements to its acquisition practices, according to the U.S. Government Accountability Office’s (GAO) Feb. 25 report, “Missile Defense Transition Provides Opportunity to Strengthen Acquisition Approach.” The GAO has been providing annual assessments of the agency’s progress since 2002.

The MDA in fiscal year 2009 went through its first presidential transition, changed directors and saw its budget request reduced by approximately $1 billion relative to the previous year’s request, the GAO said. The agency overhauled its approach to deploying a European missile shield, canceled several high-risk technology programs and started programs dedicated to knocking down missiles while they are ascending.

In 2008, the MDA changed its acquisition strategy from one based on fielding missile systems in two-year increments to a capabilities-based structure without a time component. The new strategy included several positive changes, including a commitment to establish the total unit costs for programs and an end to the practice of deferring work from one block to the next, the GAO said.

But in June 2009, Army Lt. Gen. Patrick O’Reilly, the MDA’s new director, terminated the new strategy, and he has yet to settle on another approach, the report said.

Under previous strategies, the MDA provided Congress with delivery schedules for each of its integrated missile defense capabilities. The MDA did not this year, so the GAO could not assess agency progress. The GAO noted that in its previous annual assessment, it found that the MDA was behind schedule for many of its stated goals.

O’Reilly told the GAO to expect updated timelines by the summer, according to the report.

The GAO made several recommendations to improve transparency and accountability at MDA. These included: reporting program acquisition unit costs to Congress and informing lawmakers when cost growth occurs; reporting test goals for each element of the ballistic missile defense system; and developing schedules for when each missile defense capability will be ready for operations and reporting when these goals are achieved.

The MDA agreed with each of these recommendations.

The MDA last year met many of its goals for delivering missile defense assets, the GAO said. The agency planned to deliver 41 assets across four of its systems: the Aegis Ballistic Missile Defense system; the Ground-based Midcourse Defense system; Sensors; and Command, Control, Battle Management and Communication. The GAO said 34 of those assets — or 83 percent — were delivered.

While the MDA also made progress last year in system testing, targets continue to be a trouble spot, the GAO said. During 2009, the agency demonstrated the Aegis Ballistic Missile Defense system’s ability to destroy multiple targets in an engagement, the Terminal High Altitude Area Defense system’s ability to launch multiple interceptors to destroy a single target, and the first flight tests of the fully integrated Airborne Laser, among other things. Testing progress has enabled the agency to improve its modeling and simulations capabilities, the report said.

Faulty target vehicles have been responsible for many testing delays and failures since 2006, and the agency last year began an effort to buy new, more reliable targets in a more streamlined fashion. The agency is planning new contracts for short- and medium-range targets that could be delivered in 2012, and it will start its search for new long-range targets this year in hopes of fielding them by 2013, the report said.

In response to concerns expressed by the GAO, Congress and the Defense Department, MDA revamped its testing approach last year with a new Integrated Master Test Plan that the GAO said is an improvement. Completed in July 2009, the plan detailed the agency’s test program out through 2015, whereas previous plans extended only as far as two years. The new plan also provides more time for post-test analysis, which the GAO said is necessary to validate the agency’s models and simulations.

The GAO is concerned that in some cases the MDA is approving the production and fielding of certain missile defense assets before operational testing and evaluation are completed. The MDA soon intends to approve production of the first 18 Standard Missile 3 Block 1B interceptors that will be built by Raytheon, the report said. The first flight test of this new missile variant is scheduled for mid-2011, and the contractor is still maturing some of the new technologies that the missile will feature, such as the throttleable divert and attitude control system.

The GAO recommended delaying this decision to begin manufacturing these missiles until development of the critical technologies is complete and the missile is flight tested. The MDA in its response partially agreed with the recommendation, but said the 18 missiles that are awaiting approval will be used only for testing. The GAO disagreed, citing MDA documents that indicate some will be used for testing and some will be deployed operationally on Navy ships.