By Lauren Weber

After reporting lewd and inappropriate behavior by her boss over several years, Laurie West said she was assigned to a different manager in September -- and that's when a new set of problems began.

According to Ms. West, she was "iced out" of important meetings and her marketing budget was cut, making it difficult to do her job as a sales rep for a medical-imaging company. On Dec. 3, she filed a complaint with the Equal Employment Opportunity Commission alleging sexual harassment and retaliation. Four days later, she said, she was fired.

Much of the #MeToo movement has been about emboldening people who experience harassment to come forward without fear of retribution, but data show there are negative consequences for many who do.

More than two-thirds of workers who filed sexual harassment complaints with the EEOC say they have suffered retaliation, ranging from job transfers and shift changes to getting fired, according to an analysis of more than 45,000 harassment complaints filed with the EEOC between 2012 and 2016. Of those, nearly all were ultimately fired or left their jobs voluntarily when they felt their work environment became intolerable, the analysis released Wednesday found.

More victims are coming forward, but retaliation remains a risk, data show. In the 12 months through Sept. 30, filings with the EEOC alleging sexual harassment rose nearly 14% over the prior year to 7,609 complaints. Allegations of retaliation in connection with sexual harassment have risen by about 5%, said Victoria Lipnic, the EEOC's acting head.

"It's not surprising that so few people file formal complaints given the high cost of complaining," said Donald Tomaskovic-Devey, director of the Center for Employment Equity at the University of Massachusetts at Amherst and an author of the analysis.

Researchers say the vast majority of sexual harassment experiences go unreported, and fear of retaliation is a primary reason.

Ms. West, a Florida resident, said over the course of several years, her manager made comments about her body and regularly ordered her to meet him at his boat in a bikini so they could entertain physicians. Once, she said, he got into her car with a gun and placed it on her daughter's empty car seat.

Though she reported some of the incidents to a regional manager, nothing changed for years until she shared with that manager a photo of a nude woman her supervisor had texted her.

An attorney for Ms. West's former employer, Health Management Company of America, which is majority-owned by diagnostic-imaging company Fonar Corp., described her allegations as "false and unsupported." The attorney said Ms. West had asked to be let out of her noncompete agreement and that she was terminated for downloading and sending proprietary company documents to her personal email address. The company was concerned that Ms. West would take that information to a competitor, the attorney said.

Ms. West said she had trouble accessing work emails from some of the company's servers, and that she emailed herself the documents so she could access them from her phone or laptop at any time.

"Sexual harassment is about power disparity for sex. People are interested in something beyond just harassing someone," Ms. Lipnic said, speaking generally. When harassers are rejected or rebuffed, she said, emotions flare and retaliation frequently follows.

For Sonya Harvey, a longtime employee of New York City's Department of Correction, the harassment began in 2007, she said, when she alleges a co-worker exposed himself and masturbated in front of her. Other forms of harassment followed, Ms. Harvey said, as he groped her breasts and buttocks and sent her explicit text messages. When she complained to a supervisor, she said, she was moved to a desk closer to her harasser, "where he tormented me every day."

Shortly after, she was transferred to an assignment on Rikers Island, Ms. Harvey stated in a lawsuit filed in New York state court in 2012. Her harasser also was sent to a facility on the island, the site of the city's main jail, but the department refused to reassign her, she said. She believes she was also passed over for other positions because she reported being harassed. "It's not fair," she said. "Only because I stood up for myself and reported this guy?"

The Department of Correction didn't address Ms. Harvey's specific allegations. But in a statement DOC spokesman Peter Thorne said the department had initiated new harassment training and hired more staff to investigate allegations. As a result, the number of reported allegations has fallen 31% over the past year, he said.

"Every employer I know is paying even more attention to substantive anti-harassment training and also impressing on managers that, while it may seem counterintuitive, when someone makes that complaint you cannot retaliate against them in any form or fashion," said James Paretti, formerly chief of staff to Ms. Lipnic at the EEOC and now a management-side lawyer at employment law firm Littler Mendelson PC.

For those who do report, the payoff -- if there is one -- is usually slim. While cases such as former Fox News anchor Gretchen Carlson's roughly $20 million settlement with 21st Century Fox get attention, the EEOC analysis found that only 23% of workers who file sexual harassment complaints receive some monetary compensation, and the median award is just under $10,000. Fewer than 1% of awards exceed $100,000.

That may be changing. The EEOC recovered almost $70 million for workers who experienced sexual harassment in fiscal 2018, up from $47.5 million in 2017. The agency also filed 41 sexual harassment lawsuits, a 50% increase over the prior year.

"The legal route to address sexual harassment fails for most people," said Mr. Tomaskovic-Devey.

Write to Lauren Weber at lauren.weber@wsj.com