Move comes weeks after department announced its intentions to move ahead with portions of the new system.
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Lurita Doan tells lawmakers she can't remember details of Jan. 26 meeting at a GSA facility during which political issues were discussed.
The 38-year-old program suffered massive losses in the aftermath of hurricanes Katrina and Rita.
Union hopes to expand representation of TSA employees, as rival labor organization notes it has been active in the agency for five years.
Key GOP panel member says allegations against Lurita Doan will not stand up to scrutiny.
Late changes in the law and other factors conspired to place this season among the most difficult in memory, commissioner says.
Majority of survey respondents see benefits to pay for performance systems, but many are not confident of successful implementation.
Inspector general recommends more resources, notes number of fugitives rose nearly 88 percent from 2001 to 2006.
Uncertain funding mechanisms and a poor governing structure are among the problems jeopardizing the effort to create a wireless network for first responders.
Departure comes amid controversy over unauthorized spending on items such as private jet travel.