Sarah Pierce became an aid worker because she wanted to help eradicate disease in Africa. While working in a remote field office in South Sudan, she was raped in her tent by a fellow aid worker.

Three months later, her contract was terminated. Pierce, 27, says her employer, the Carter Center, a major American NGO, told her she was not suitable for work in the field. Pierce says she was fired because she was openly critical about her employer’s failure to support her properly or help her seek justice.

It was in December last year, while Pierce was working on a project in a remote area of South Sudan, that she says she was attacked. She was living in a tented compound with other men and women from local charities. On her last night before a contract break she says a colleague “came into my tent while I was asleep and climbed into my bed naked and raped me”.

Pierce reported the attack to a superior in a phone call the following day. “I was exhausted in pain and probably in shock,” said Pierce (not her real name). “The first thing she asked me was why no one had heard me scream. I was questioned as to why I hadn’t reported it directly to the staff of the local non profit – all men, some of whom reported to the man who raped me – or why I hadn’t told my driver or programme officers – all male.

“She wanted to know why my tent hadn’t been locked, why had I been in the compound and why I didn’t call and report it immediately as it happened? Why I didn’t fight back more?”

Pierce said the response exacerbated the trauma she felt. “It wasn’t ‘Are you OK, do you need medical attention?’”

The aid worker said she was not offered any immediate medical care or legal options by the superior. “She asked if I had led him on. As soon as she asked the question I automatically did not want to disclose anything else.”

I felt like I was fired because I was raped

When Pierce went back to work after her contract break, she spoke openly about the incident with other international staff, partly to help her deal with the trauma but also to warn colleagues of the risk. “I was told very clearly not to talk about it,” she said, adding that one of her managers made it clear that it was up to the organisation to decide how openly the incident should be discussed.

Three months after the attack she was called to the capital, Juba, for a meeting.

“I went down thinking it was an opportunity to discuss how to make a better policy,” said Pierce. “But (her superior) was so defensive and said that the procedures we had were appropriate. I just needed to learn how to handle it, and if I continued to speak out about it, Carter Center would not be comfortable having me in the field.”

The following day the superior called Pierce to say the organisation had decided not to honour her contract. “I felt like I was fired because I was raped,” she said. “I felt so disappointed and betrayed. I didn’t expect them to protect me from everything, but I expected that if something happened they would treat me decently and with respect.”

A Carter Center spokeswoman said the assault was a “personal tragedy and an affront to all aid workers”. “Actions we took were driven by concern for her welfare. She was provided medical treatment and encouraged and supported to seek counselling, including flights for that help to Nairobi. She is the victim of a tragedy, and the Carter Center does not wish to add any further or unnecessary suffering through a public medium, even if she gave you permission to contact us.”

The spokeswoman said the Carter Center’s protocols for field operations were informed by nearly 30 years of experience working in or near areas of conflict or with unstable governments. The Center did not comment on the reasons for Pierce’s dismissal, nor on her claim that she was instructed not to talk about the rape to other colleagues, citing the need to maintain confidentiality.

Pierce’s experience is at the extreme end of the spectrum of sexual harassment and violence within the humanitarian world, an issue specialist psychologists and those working within the sector say is hugely underreported.

Most of those who have come forward to the Guardian are women, but men are also victims. Many say they are afraid to speak out because they fear being ignored, treated as troublemakers or causing damage to their professional reputation.

Julia Hernandez, 28, a Brazilian aid worker has worked for several UN agencies and non-governmental organisations in Africa. She said: “I have seen senior men in a senior UN meeting taking a picture of the breasts of some young consultant across the table. I have had colleagues call me on my office phone to tell me they like the dress I’m wearing. I’ve seen so much of it. I feel harassed either by colleagues in my office or out in the field. It becomes tiring.”

Hernandez, whose name has been changed because she fears repercussions for her career, said the culture made it difficult for women to do their jobs. “We ask, why don’t we have more women in the office? But no young women will ever feel comfortable working in such an environment.”

Many women who have experienced sexual abuse say the failure of the agencies and charities to take the issue seriously makes the experience worse.

In Kabul, Josie Tillford – not her real name – was working for a US Aid contractor and felt like “one of the boys” with her mostly male colleagues until she was sexually assaulted in June at a work event. Colleagues were supportive initially. But she said they wanted her back at work at full capacity and would not allow her talk about the attack.

“My boss said, let’s keep it among us. He didn’t want gossip,” she said. “Not being able to talk about it made dealing with it difficult. I started having a stress reaction: had a hard time sleeping and nightmares. I tried to say to my colleagues that I was having a difficult time. It was suggested that I reach out and find counselling on my own. But what I was really trying to say was, ‘I need a break. I’m emotional. I’m sad because of this.’ It was misunderstood. There was a lot of tension and maybe some hostility.”

We have to be quite careful with applying what we see as universal values that are very western-centric

Zehra Rizvi, a humanitarian consultant who has worked in the sector for 10 years, said culture was never an excuse for ignoring sexual abuse and intimidation. “You have to respect people. It might be part of your cultural normality but that doesn’t mean that it’s OK. I think there are universal values and maybe we hide behind the cultural aspect.”

Katy Harris, another female security expert, experienced difficulties with men on her team while working for German development agency GIZ in Asia. “It started with spreading rumours about my personal life,” said Harris, who asked for her real name to be withheld for fear of repercussions.

Then the three men came to her house at 10pm on a Monday with a cake. “My litmus test was would they behave this way with a local woman and I knew the answer was no, they knew I lived alone, so I didn’t let them in.”

Harris says she raised the issue with her GIZ manager but claims he dismissed her concerns, she said. “He made me feel like I was imagining things.”

In the end Harris tackled the men herself. “I lost my rag because it had been going on for so long. It wasn’t the best way to respond to it but my boss hadn’t done anything.” Addressing the men’s behaviour directly, however, just made it worse. “It was the worst two years of my life … I didn’t trust those colleagues and when you’re working in insecure environments, you need to feel that people have your back.”

A GIZ spokesperson said the organisation had a policy banning sexual harassment in its offices in Germany and abroad. It insisted “staff members treat and communicate with each other with respect, regardless of their contractual status or position in the hierarchy”.

The spokesperson added: “GIZ takes all incidents of sexual harassment extremely seriously. Appropriate disciplinary action will be taken in verified cases of sexual harassment … Managers are responsible for maintaining a working environment free of offensive behaviour.”

Pierce is working in another country for a different organisation now, but the rape still haunts her. “I honestly don’t know how much longer I will be able to do this kind of work.

“This is the career I’ve been working towards for the last 10 years. But It’s a real challenge to figure out what I can live with.”

This article was amended on 19 October 2015. A claim by an agency worker was removed because a response from the organisation concerned had not been sought regarding the allegation.

Guardian Global Development Professionals Network is running a series on this and other issues affecting aid workers. Email globaldevpros@theguardian.com to share your story

