Pentagon officials said difficulties are being addressed, and will be ultimately solved by the Defense Travel System.
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Sen. Carl Levin, D-Mich., said the Defense Department should build trust if it wants the new National Security Personnel System to succeed.
Defense officials tell Senators that more information will emerge during upcoming "meet and confer" period.
About 15 percent of civil service workforce will be transferred or paid to leave by end of fiscal 2006.
Federal personnel officials will get together with union negotiators Thursday to iron out the details of the meet and confer period.
Ways and Means Committee Chairman Bill Thomas, R-Calif., is a powerful voice against a bill that could save federal retirees an average of $400 annually.
Merit Systems Protection Board officials say provisions in the new Homeland Security personnel system require the agency to start giving priority to its cases.
Rep. Steny Hoyer, D-Md., told union members Wednesday that the Bush administration is trying to do away with collective bargaining.
Pentagon official notes DoD plans to spend $130 billion of its $419 billion fiscal 2006 budget request on military personnel and health care.