Former Pentagon General Counsel Jeh Johnson won Senate approval on a 78-16 vote.
Confirmation had been slowed by an unrelated dispute over providing information to Congress about the A-10 program.
Some of the legislative proposals are in conflict with reorganization plans unveiled earlier this month by Defense Secretary Chuck Hagel.
A coalition of industry groups is asking lawmakers to keep supply-chain restrictions out of upcoming funding bills.
The idea is to create an incentive for agencies to relinquish spectrum as part of a plan to free up 500 megahertz for commercial use by 2020.
The measure targets critical infrastructure protection while providing no new regulatory authority for the Department of Homeland Security.
The HHS secretary is also calling for the creation of a chief risk officer position at the Centers for Medicare and Medicaid Services tasked with reducing risks associated with major policy initiatives.
The final deal calls for $1 trillion in spending for fiscal 2014, reduces sequestration cuts, adds money for defense and domestic programs, and requires newly hired federal employees to contribute more to their retirement plans.
A revised version of the Pentagon policy bill could be considered in the House this week, but IT acquisition reform will have to wait until at least 2014.
Open letter urges Congress and the president to ensure U.S. surveillance efforts are "restricted by law, proportionate to the risks, transparent and subject to independent oversight."
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