"Today I resigned as director of the Federal Emergency Management Agency. As I told the president, it is important that I leave now to avoid further distraction from the ongoing mission of FEMA," said Brown, who was also the undersecretary for emergency preparedness and response for the Department of Homeland Security.
The announcement seemingly came as a surprise to President Bush, who was touring hurricane-ravaged Louisiana and Mississippi.
"Maybe you know something I don't know. I've been working," Bush said when asked by reporters about the news. Bush said he planned to talk with Brown's boss, Homeland Security Director Michael Chertoff, from Air Force One on the flight back to Washington.
Bush, however, was not likely taken unaware by the announcement since within two hours, the White House published a statement saying the president intended to nominate R. David Paulison, head of FEMA's emergency preparedness force, to lead the agency.
During the return flight to Washington, White House spokesman Scott McClellan said the president appreciated Brown's service.
"Mike Brown has done lot of great work on a number of hurricanes. Last year there were four hurricanes to hit Florida and he was widely praised for FEMA's response and recovery efforts. Hurricane Katrina has been an unprecedented storm and has presented us with enormous challenges, many of which we are beginning to address," McClellan said.
Brown told The Associated Press that he spoke with Bush before he was called back to Washington last week and indicated that he had suggested to the president that he call it quits. He added that he spoke on Saturday to White House Chief of Staff Andy Card, who did not request his departure.
Brown said he feared he was becoming a distraction to FEMA's relief effort.
"I came to the conclusion that this was in the best interest of not just the administration and not just me, but FEMA," he said. "They need to be focused on the continuing efforts in the Gulf."
In his statement, Brown added that he was honored to have worked at the agency.
"There is no other government agency that reaches people in a more direct way. It has been the best job in the world to help Americans in their darkest hours," he said.
Brown's decision should come as no surprise to most. On Friday, Brown was unceremoniously recalled to Washington after being the lead official in charge of federal emergency operations in the Gulf Coast region.
The no-confidence vote was one of the latest indicators that the U.S. government was trying to revamp its image in the face of grueling criticism over the slow pace of federal relief operations.
Shortly after Brown was recalled, officials close to the FEMA director said he would likely resign. They said that even before Katrina, Brown had been planning on leaving the administration late this fall to go into the private sector.
Department of Homeland Security officials who spoke to FOX News could not say whether the resignation was effective immediately.
Senate Majority Leader Bill Frist said he did not know the details of the decision, but looked forward to talking to Brown.
"It was both a personal and professional decision, I do wish him and his family well," Frist said.
House Minority Leader Nancy Pelosi of California said she was pleased with the decision.
"The American people deserve new professional leadership at FEMA. Michael Brown's departure from FEMA is long overdue, and his resignation is the right thing for the country and for the people of the Gulf Coast states," she said.
Senate Minority Leader Harry Reid said that Brown's resignation does not resolve the problems of the administration's handling of hurricane relief efforts. Democrats have been calling for an independent commission to investigate FEMA's shortcomings. But House and Senate Republicans have wanted to appoint a special committee to analyze what went right and wrong with the federal response.
Frist said that he and Speaker Dennis Hastert had discussed convening a panel that would be assigned with making recommendations on how to prepare and respond to natural disasters even though Democrats have not signed on yet to their plan.
"Our responsibility here at the United States Senate is oversight, is analysis, is [to] determine what's working and what's not working so I am confident at the end of the day the Democrats will come to the table to participate. It's our responsibility, it's what the American people expect," Frist said.
FOX News' Jim Mills and Sarah Herndon and The Associated Press contributed to this report.