Back in his old job at the Pentagon last week after more than a decade, A. Ernest Fitzgerald paused before answering the question: "Would you do it again?"

The man who has been called the nation's "No. 1 whistle blower" said he used to respond, "Yes, of course, I'd do it," automatically. But now he likes to savor that question before he answers it, no matter how many times reporters have asked.

"Some people tend to emulate me," the 55-year-old bureaucrat explained, "but there is nothing glamorous about losing 14 years of your life."

Fitzgerald "lost" those years because he told the truth at a congressional hearing Nov. 13, 1968--disclosing for the first time in public that the C5A military transport would cost $2 billion more than the Defense Department's original contract.

His bosses didn't care that Fitzgerald, a civilian management systems deputy to the assistant secretary of the Air Force for financial management, was under oath and had been asked about the cost of the aircraft. The day after he disclosed the cost overruns, he recalled, doors at the Pentagon began slamming shut.

For one year, Fitzgerald was ostracized by his peers and shadowed to and from work by an unmarked sedan. His mail was opened and fictitious conflict-of-interest charges were put in his personnel file. He was given unimportant work, and then, he was fired.

Fitzgerald sued the government to get his job back--his first government job and one that he had held for three years. He then sued President Nixon who, he claimed, had ordered him fired.

Looking back on the publicity that surrounded his battles with the government, Fitzgerald said, "It's silly to make such a big to-do about someone who has told the truth . . . . The least that taxpayers should expect from government employes is the truth. The fact that the truth is so rare shows that the government's approach has been backwards."

The government, he said, should stop passing ineffective laws to protect whistle blowers and begin punishing employes who "lie, cheat and steal." Most government officials are "not brave enough" to risk going to jail "if they really thought they would be sent there."

In 1973, the Civil Service Commission ordered Fitzgerald reinstated with back pay, but he sued a year later, claiming that his job was not as good as the one he had had before he exposed the overruns.

In May, 1980, Nixon agreed to pay him $142,000 to avoid having the case go to trial. The agreement was reached after Fitzgerald's attorneys received transcripts of White House tapes that they said alluded to Fitzgerald and quoted Nixon telling his aides to "get rid of that son of a bitch."

Last week, a district court judge ordered the government to reinstate Fitzgerald to the same job that he had held when it all began. While he said he was thrilled to get it back, Fitzgerald said the victory was bittersweet because he doesn't believe whistle blowers today are any safer than they were in the late 1960s. The government, he explained, hasn't learned anything.

"People call me and tell me about things that are wrong in government," Fitzgerald said. "They say they would do the right thing report it if they could get away with it. Now, that's a sad commentary because, in fact, most of them don't believe they can get away with it."

Congress has done little to fight that fear, he added.

The Civil Service Reform Act of 1978, which Fitzgerald calls the "Civil Service Deform Act," is "Jimmy Carter's joke on American taxpayers," he said. It lacks any real teeth to protect whistle blowers, Fitzgerald said. The Office of Special Counsel, which the act created to investigate complaints of harassment of whistle blowers, is "clearly a sting operation," he contended.

"It's purpose is clearly to identify and deal with troublemakers. The whole process is a sham."

If Congress had been serious about protecting whistle blowers, Fitzgerald said, it would have given the special counsel's office the power to file disciplinary cases against presidential appointees. Under current law, if the office finds that a presidential appointee has violated a prohibited personnel practice--such as firing or harassing a whistle blower who has embarrassed the administration--its only recourse is to file a report with the president. The special counsel's office, which is directed by a presidential appointee, has never undertaken such a probe.

Fitzgerald always has been critical of the reform act. Recently, others have joined him. Last month, Rep. Patricia Schroeder (D-Colo.) and several groups that had strongly endorsed creating the special counsel's office said it should be abolished because it has become a "fraud."

Based on his experiences, Fitzgerald said he believes punishing whistle blowers is inbred in Washington. "Washington is a one-industry town, just like steel was the one industry in the town where I grew up," Fitzgerald explained, "only the industry here is politics . . . and everyone knows that the lifeblood of politics is patronage.

"Dispensing patronage in whatever form possible, whether it be tax breaks, water projects, changing regulations, et cetera--that's the name of the game in this town and any bureaucrat that gets in the way of patronage is in trouble."

What does Fitzgerald tell would-be whistle blowers who contact him? "I don't give advice. . . . It's a choice you have to make yourself. . . . Others will never have the legal resources that I had," he explained, referring to the legal support he got from the American Civil Liberties Union and the local law firm of Howrey & Simon. His legal expenses totaled close to $1 million.

So what will he do now if he uncovers another C5A?

"I'm not a closet patriot. . . ," he said, "who leaks documents to the press or Congress. I would try to work within the system." But when a Hill subcommittee asks the question this time, he said, "I would have a job lined up and a lawyer ready."