The cause was congestive heart failure, his son Charles said.
Mr. Beggs was named administrator of NASA by President Ronald Reagan in 1981. He was on administrative leave — to defend himself against accusations, later declared baseless, of overcharging the government — when Challenger sundered 73 seconds after liftoff, killing seven crew members, including a high school teacher, Christa McAuliffe.
Mr. Beggs had been replaced at the time by a “White House political appointment,” and “NASA was thus bereft of experienced and trusted leadership” when Challenger exploded, according to an official NASA history written in 1998 by Prof. John M. Logsdon, the former director of the Space Policy Institute at George Washington University.
Mr. Beggs had championed the shuttle program during his tenure, charming conservative critics of big government, especially a president whom he once described as “almost technically ignorant.”
In 1985, Reagan was invited to Edwards Air Force Base in California to see the retired shuttle orbiter Enterprise, mounted on a Boeing 747, flown back to the Kennedy Space Center in Florida for public display.
“I said, ‘After you finish your speech, just say, ‘Enterprise, you’re free to roll,’” Mr. Beggs told Reagan, as he recalled in a 2002 oral history interview. “That 747 will rev up and it’ll come roaring by and take off.”
“He said, ‘I can do that?’ I said, ‘Yes, sir.’ So he did, and when he left that day, he said, ‘That’s the most fun I’ve had since I got this job.’”
Mr. Beggs shepherded the space shuttle from its experimental stage to what he called an operational phase, promoted the development of an International Space Station and was crediting with lifting morale in an agency that had known little recent glory.
After a successful shuttle mission in 1982, he said, “We’ve proven once again that when we want to, we can perform splendid things and make them look easy.”
Before joining NASA as its administrator, Mr. Beggs was the under secretary of transportation from 1969 to 1973 under President Lyndon B. Johnson. In that post he oversaw the creation of Conrail, which reorganized the freight operations of the bankrupt Penn Central Transportation Company and Erie Lackawanna Railway, and initiated Amtrak as a quasi-public passenger railroad.
Mr. Beggs tried unsuccessfully to create an American version of a commercial supersonic plane. And while he believed that “there must be intelligence out there somewhere” in outer space, his prediction that contact would be made by the beginning of the millennium proved unfounded.
James Montgomery Beggs was born on Jan. 9, 1926, in Pittsburgh to James Andrew Beggs, a bookkeeper and accountant for an oil well supply company, and Elizabeth (Mikulan) Beggs.
After attending Southern Methodist University in Dallas for a year, he entered the United States Naval Academy, where he graduated in 1947. He served in the Navy as a pilot and submariner until 1954 and earned a master’s degree in business administration from Harvard Business School in 1955.
He married Mary Harrison, who became chairwoman of the Wolf Trap Foundation for the Performing Arts in Virginia; she died in 2015. In addition to their son Charles, he is survived by another son, James H. Beggs; two daughters, Maureen Fox and Terri Luechtefeld; and 10 grandchildren. Another daughter, Kathleen Beggs, died in 2012.
After serving as transportation under secretary, Mr. Beggs was an executive with Howard Hughes’s Summa Corporation. In 1974, he was named an executive vice president of General Dynamics, the government defense and aerospace contractor. In 1985, General Dynamics along with Mr. Beggs and three current company executives were indicted on charges of overbilling the Army for millions on a weapons contract from 1978 to 1981, when Mr. Beggs was an executive with the company. He went on administrative leave from NASA and never returned.
He resigned from NASA in 1986, about a month after the Challenger disaster, and in 1987 all the federal charges were dropped. A year later, Attorney General Edwin Meese 3d publicly issued what he called a “profound apology” to Mr. Beggs, explaining that the indictment had been based on “an inaccurate understanding and assessment of the underlying facts.” He added, “Your fellow citizens should now be more aware than ever that your character is untarnished and your behavior unblemished.”
Even before the indictment and the Challenger disaster, Mr. Beggs had to grapple with political second-guessing and skepticism about scientific progress.
He recalled the firestorm that ensued after Tom Hayden, a California state legislator, and his wife, Jane Fonda — who were both known for their liberal activism — were invited in 1983 to watch as the astronaut Sally Ride became the first American woman to be launched into space. Mr. Hayden represented the district in which Ms. Ride’s parents lived. Mr. Beggs said that he and his wife were never invited to the White House by the Reagans again.
While he was reluctant to rehash NASA’s culpability in the Challenger accident, Mr. Beggs said “they shouldn’t have launched” and that, despite being on leave, he had called the agency’s chief engineer that morning to express concern about icing.
“Whether I would have done anything different at the time, I’ve thought about that,” he said. “I think I would have, but that’s pure conjecture.”
The shuttle was “the most reliable and safest space vehicle we’ve ever flown,” he added. “No flying machine is 100 percent safe.”