Three days after his arrest on a drunken-driving charge in Fairfax City, J. Randolph Babbitt resigned as head of the Federal Aviation Administration on Tuesday.

“Today I submitted my resignation to Secretary Ray LaHood and it has been accepted,” Babbitt said in a written statement. “Serving as FAA Administrator has been an absolute honor and the highlight of my professional career. But I am unwilling to let anything cast a shadow on the outstanding work done . . . by my colleagues.”

Babbitt’s ouster seemed inevitable after LaHood, the transportation secretary, first learned of the arrest from a police news release more than 36 hours after the incident.

“What I told Randy is that I was very disappointed with the way that I learned about this,” LaHood said Tuesday afternoon, hours before Babbitt’s resignation.

Babbitt’s departure, less than halfway through his five-year term, leaves the FAA in turmoil, beset by a series of recent stumbles, facing funding uncertainty and tasked with developing a $40 billion guidance system based on the Global Positioning System that is expected to revolutionize air travel.

Randy Babbitt in a Fairfax County Sheriff's booking photograph. (REUTERS)

Given LaHood’s mantra of “safety” above all else and his commitment to combating drunken driving, he was thrust into an untenable position.

“As FAA Administrator, Randy Babbitt has been a dedicated public servant and outstanding leader,” LaHood said after the resignation.” On behalf of the American people, I thank him for his service and his leadership.”

Babbitt was pulled over about 10:30 p.m. Saturday by an officer who saw him driving alone on the wrong side of the road on Old Lee Highway, a four-lane thoroughfare about nine miles from his Reston home, police said.

Police did not release Babbitt’s blood-alcohol level, but .08 is the threshold to bring charges of driving while intoxicated in Virginia. He is scheduled to appear in court on Feb. 2.

In addition to losing his job, Babbitt will lose the pilot’s license he has held for more than half his adult life if he is convicted and loses his state driver’s license. He served as an Eastern Air Lines pilot for 25 years.

Aware that the Fairfax City police are required to make public DWI arrests of public officials, Babbitt made what may be his final flight at the controls of an airplane Monday morning.

Babbitt and an FAA pilot boarded an FAA Cessna Citation designated as “November 2” and flew out of Reagan National Airport. With Babbitt in the co-pilot’s seat, the plane flew for hours, returning in early afternoon as news of his arrest became public.

President Obama appointed Babbitt, 65, in 2009. His tenure was marked by challenges, and he won high marks from the unions, airlines, Congress and his senior staff for his steady hand in weathering the storm.

The agency was on the mend from a protracted confrontation with the air traffic controllers union that had just been settled with a new contract.

He sought to make peace with the union while changing the FAA culture. A centerpiece of that innovation was a non-punitive system in which controllers were encouraged to report their own mistakes. Implementation of the system coincided with a big increase in the number of mistakes nationwide.

They included high-profile errors such as one involving first lady Michelle Obama.

As he wrestled with that controversy, another one exploded when an air traffic controller in the tower at National slept while several pilots of late-night flights landed without assistance.

The issue caught fire on talk shows and with TV comedians as controllers were discovered sleeping on the job at several other airports.

Babbitt fired some and tinkered with scheduling practices that left controllers drowsy.

He turned the controllers division over to David J. Grizzle, the FAA’s legal counsel, and brought in a new man to serve as the FAA’s No. 2 administrator.

That administrator, Michael P. Huerta, steps in as acting administrator and inherits Babbitt’s problems and challenges.

Congress has not passed a long-term funding bill for the FAA since the last one expired in 2007. Instead, as Congress has quibbled over a handful of relatively minor issues of little interest to the flying public, the FAA’s planning has been hamstrung by 22 extensions.

That was problematic as Babbitt sought to persuade airlines to invest billions as their share of the new NextGen system. The airlines pointed to the stalemate and questioned whether the FAA could deliver on the deal.

“His departure creates a serious setback, leaving the FAA in limbo at a critical time for the agency,” said Rep. John L. Mica (R-Fla.), chairman of the House transportation committee.

Staff writer Mary Pat Flaherty contributed to this report.