Two lawmakers introduce amendment to improve process for granting port security clearances.
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BRAC panel members express concern about impact of stripped down bases on local communities.
Portsmouth Naval Shipyard would lose largest number of civilian jobs.
Recommendations also include realigning 29 major facilities; other bases will gain troops.
CBP Commissioner Robert Bonner says thousands of more border guards are needed.
Some of the service's oldest and best-known bases are slated to be shuttered or restructured.
Large facilities in Connecticut, Maine and New Jersey slated for closure, with thousands of jobs at stake.
The recommendation would involve closing 21 Defense Finance and Accounting Service facilities.
At issue is provision in fiscal 2006 Homeland Security spending bill not to fund President Bush's proposal to create a new office for coordinating screening efforts.
Nearly 67,000 civilian jobs are slated to move to new locations.