IN THE 16 months since Barbara Honegger was brought to the Justice Department as a $37,000-a-year special assistant, she says, she met her boss once. On the day she was hired. She says she met the second-in-command of the department's civil rights division, where she works, once. Accidentally, at a party.

No doubt yesterday Assistant Attorney General William Bradford Reynolds and his deputy Charles J. Cooper knew who she was. In an opinion page article in Sunday's Washington Post, Honegger spun herself into national prominence by denouncing the Reagan administration's program to create an alternative to the proposed Equal Rights Amendment, characterizing it as "a sham."

Honegger says she is a policy analyst.

A Justice spokesman says she's a technician with no appreciable authority.

In a town that prides itself on political loyalties, rarely do government bureaucrats throw rocks at the person who is still paying their salaries. Honegger's accusations come at a particularly touchy period, when the administration is undertaking a concerted effort to rebuild its relationship with women voters and bridge the so-called "gender gap."

"He doesn't deserve loyalty," says Honegger of Reagan, "because he has betrayed us. That is not too strong a statement."

Late yesterday afternoon, Honegger, 35, sat nervously in a friend's Georgetown apartment explaining why she went public with her charges. Also at the apartment offering moral support was Mary Crisp, another disenchanted Republican who garnered headlines in 1980 by publicly complaining about her party's positions on ERA and subsequently leaving her job as co-chairman of the Republican National Committee.

Honegger hasn't been faced with that decision yet. The publication of yesterday's article coincided with the beginning of her two-week vacation. Indeed, her job, a political appointment, expires Sept. 30.

"Part of what led me to do precisely what I did was to know that media attention would get them to fulfill their own promise," said Honegger in a high-pitched schoolgirl voice. In the Reagan administration, she says, women's rights have "the lowest possible priority."

She is certainly getting what she wanted. Yesterday she was interviewed by CBS, NBC and National Public Radio and was scheduled to appear on both "Good Morning America" and the "Today" show this morning.

Said Crisp, a friend of Honegger: "Two months ago she had this in mind. She knew the president was not sincere. She didn't know quite how to do it or what to do."

Honegger comes across as a modern day Pollyanna--chatty, pert and a do-gooder. She is dressed in a high-neck navy blue dress and practical navy pumps. Her auburn hair is cut bluntly in a traditional pageboy. She fidgets with some notes while she talks and is frequently guided by her friends when she strays from the point.

She describes herself as a "zealot" and says her decision to go public was in keeping with how she has lived her life. Her father, a contractor, and her mother are longtime Republicans, she says. Honegger, who is single, says she is very religious. She recently joined the Methodist church and attends services every Sunday near her home in suburban Virginia.

"I'm an activist," she says, noting that she was a straight-A student at a Hanford, Calif., high school; at the University of California at Berkeley, where she studied creative writing; and at the John F. Kennedy University in Orinda, Calif., where she received her MA in psychology. She says she is not a politician, and, in fact, only entered the political arena when she joined the Reagan campaign in 1980.

She says she first met Reagan in 1976 at the Hoover Institute, where he was visiting Martin Anderson, then a fellow there. Honegger was a researcher for Anderson. Later, when Anderson became head of the White House domestic affairs office, he brought Honegger to Washington with him.

"Personally what I get out of going public is knowing that I have saved equal rights for women, and I would also very much like to redeem the Republican Party from the far right . . . Somebody has got to tell the truth . . . Believe me, I knew there would be consequences, but there are some times in your life when you realize you have no choice but to act. My conscience dictated that I do this. I had no choice."

She is, she says, head of the attorney general's Gender Discrimination Agency Review, which amounts to a computer search of federal laws that discriminate by sex and those that forbid sex discrimination. Honegger says she hand-delivered a report containing the lists of those laws, as well as statements from 17 federal agencies on their policies on sex discrimination. She claims the administration took no action on her report. (White House spokesman Larry Speakes has said that the report was not completed and would not be until next April. Honegger says the report she submitted is missing only reports from the 24 other federal agencies and that virtually all that material would be compiled by September.)

"She is not a policy-level official," said Justice Department spokesman Tom DeCair yesterday. "She's not a lawyer . . . It's a technical job . . . She was sent over to the Justice Department as one of several people to contribute to periodic reports on legal issues . . . She is not the project director of anything . . . This Gender Discrimination Agency Review--we never even heard of it . . . It doesn't exist. I'm surprised The Washington Post devoted half a page in Sunday's newspaper to a low-level functionary with no policy role in the administration and who admits in her own piece that she is a disappointed job seeker . . ."

DeCair said she won't be fired because her job ends next month--"she's a consultant."

Honegger, when told this, countered by reading her job description, which specifies, among other things, that she "participates in the formulation of Civil Rights Division programs and policies concerning sex discrimination."

"Even the densest human being, after a year of nothing happening, gets the message Reagan reneged on his promises. I am incensed. It was an easy decision to make since I realized what the truth was--that he didn't care about equal rights for women. I realized they were buying time and they didn't intend to do anything . . ."

She denies that she acted out of a sense of self-promotion.

"It's not true. I know myself. I know why I've done what I've done. I've done it for all those women out there who are buying a lie--that Ronald Reagan believes in equal rights for women but just doesn't support the Equal Rights Amendment. That is a lie . . . It took me all this time to realize that I had been had."