Mary Cain of the U.S. runs during the 3000m final during day three of the IAAF World Junior Championships at Hayward Field on July 24, 2014 in Eugene, Oregon.

Nike has been hit with another damning op-ed, highlighting the obstacles female athletes have faced through training with the company.

This one targets Nike's Oregon Project, coached by Alberto Salazar, previously the best track team in the world.

"I joined Nike because I wanted to be the best female athlete ever. Instead I was emotionally and physically abused by a system designed by Alberto [Salazar] and endorsed by Nike," Mary Cain said in an op-ed in The New York Times.

Cain said she was met with an all-male staff when she arrived at Nike to train, who told her that in order "to get better" she had to be "thinner and thinner and thinner." She said there was no certified nutritionist helping her and her teammates. She said Salazar told her she needed to weigh 114 pounds. Cain said she broke five bones after she lost her menstrual cycle. She said she developed suicidal thoughts and started cutting herself under all of the pressure to perform.

"[Nike] is not acknowledging the fact that there is a systemic crisis in women's sports and at Nike, in which young girls' bodies are being ruined," Cain said.

A Nike spokesperson told CNBC in an emailed statement: "These are deeply troubling allegations which have not been raised by Mary or her parents before. Mary was seeking to rejoin the Oregon Project and Alberto's team as recently as April of this year and had not raised these concerns as part of that process. We take the allegations extremely seriously and will launch an immediate investigation to hear from former Oregon Project athletes. At Nike we seek to always put the athlete at the center of everything we do, and these allegations are completely inconsistent with our values."

In an email to the Times, Salazar said he denied many of Cain's claims.

Earlier this year, the U.S. Anti-Doping Agency banned Salazar for four years, on counts of three doping code violations, though the coach has denied any wrongdoing. It was also reported in early October that Nike CEO Mark Parker had been briefed, multiple times, by Salazar on his experiments with performance-enhancing drugs. Parker responded to those allegations by calling the accounts "highly misleading." He said Nike "looked into these allegations [about Salazar] and did not find that he violated any rules."

Then Nike announced, later last month, that it was shutting down the Oregon Project entirely.

But Cain said she isn't sure that will fix the underlying issues.

"You can't just fire a coach and eliminate a program and pretend the problem is solved," the runner said. "My worry is that Nike is merely going to rebrand the old program and put Alberto's old assistant coaches in charge. ... We need more women in power."

Cain's op-ed follows a slew of other Nike female athletes speaking out this year.

A Times piece published in May included the voices of two former Nike runners, Kara Goucher and Alysia Montano, who said their contracts were cut during their pregnancies. Olympic champion Allyson Felix later that month wrote an op-ed telling a similar story.

"We've recognized Nike can do more, and there is an important opportunity for the sports industry collectively to evolve to better support female athletes," a company spokeswoman said at the time. Nike also responded by revising its contracts to include more protections for pregnant athletes, extending the period during which women's pay can't be slashed postpartum.

All of the public scrutiny makes the timing of Parker last month abruptly announcing his resignation as CEO somewhat obscure. He's set to step down in 2020. Parker also has told CNBC the decision wasn't prompted by the recent doping allegations.

Nike shares were up less than 1% on Thursday morning. The stock has rallied more than 21% this year.

Watch the full video op-ed from The New York Times here.