Rod Beckstrom, a former Silicon Valley entrepreneur, said in his resignation letter that the NSA's central role in cybersecurity is "a bad strategy" because it is important to have a civilian agency taking a key role in the issue. The NSA is part of the Department of Defense.

The power battles Mr. Beckstrom describes in his resignation letter illustrate the challenges ahead for the Obama administration as it plans its defense against governments and terrorists who might try to disrupt U.S. computer systems, cybersecurity specialists said. One issue is what part or parts of the government should lead the effort.

The Bush administration last year started a cybersecurity initiative to protect government networks, which was estimated to cost at least $6 billion in 2009 and $30 to $40 billion over the next several years. The Obama administration is conducting a 60-day review of that effort and related policies. The reviewers, led by the official who started the cyber initiative for the Bush administration, are expected to issue recommendations next month.

Mr. Beckstrom's National Cybersecurity Center, created last March to coordinate all government cybersecurity efforts, answered to the secretary of homeland security.

In reality, "NSA currently dominates most national cyber efforts," Mr. Beckstrom wrote to Homeland Security Secretary Janet Napolitano on Thursday. "While acknowledging the critical importance of NSA to our intelligence efforts, I believe this is a bad strategy on multiple grounds."

He added that "the threats to our democratic processes are significant if all top level government network security and monitoring are handled by any one organization (either directly or indirectly)." That echoed the view of some privacy advocates who worry about a government agency having too much information on individuals.

NSA spokeswoman Marci Green declined to comment on the resignation letter. Mr. Beckstrom declined to comment.

Some Homeland Security officials said Mr. Beckstrom's criticism stemmed from personality clashes and an inability to adapt to the way business is done in Washington.

Department of Homeland Security spokeswoman Amy Kudwa said that the Department of Homeland Security has "a strong relationship" with the NSA. Homeland Security "continues to work in close collaboration with all of our federal partners on protecting federal civilian networks, and is fully engaged in the 60-day cybersecurity review," she said.

Ms. Kudwa declined to respond to Mr. Beckstrom's specific critiques. "We thank Rod for his service, and regret his departure," she said.

In his letter, Mr. Beckstrom said his office was funded for just five weeks out of the past year and had just five people working in it. During the rest of the period, he borrowed staff and office space from other agencies.

Despite the lack of funding, Mr. Beckstrom said his center delivered a number of cybersecurity tools, The White House's Office of Management and Budget declined to comment.