Most New York City prosecutors’ offices rejected a greater percentage of sex crime cases in 2019, the last year for which reliable data is available, than they did roughly a decade earlier, before the case against Harvey Weinstein touched off a national reckoning.

In the Manhattan district attorney’s office, prosecutors dropped 49 percent of sexual assault cases in 2019 — among the highest rates in the city, and an increase from 37 percent in 2017, state data shows. Only the Bronx rejected a greater percentage of cases. The data excludes most sex crimes against children, and certain nonviolent offenses like stalking.

The low prosecution rate partly reflects the inherent challenges of prosecuting sexual assault, particularly cases like Ms. Duong’s, in which the attacker is not a stranger and alcohol is involved. For cases that are not dropped, conviction rates for sexual assault cases are typically much lower than for other violent crimes: 44 percent in Manhattan in 2019, compared with 79 percent for first-degree murder.

“There aren’t really any third-party witnesses to these things,” said Carl Bornstein, a former state and federal prosecutor who teaches at John Jay College of Criminal Justice. “This is tough sledding. The prosecutor has to assess: is this going to hold up under the scrutiny of 12 people?”