The Foreign Office has been forced to rewrite its guidelines on assisting victims of torture after admitting a series of failings in the case of a British woman who was allegedly raped by an Egyptian army officer earlier this year.

Tanya – a 33-year-old humanitarian worker and peace activist whose name has been changed to protect her identity – says she was sexually assaulted after being stopped at a security checkpoint near the town of El Arish, on the northern coast of the Sinai peninsula. She contacted the British embassy in Cairo for help, but claims diplomatic staff "completely failed" to offer any assistance and says they insisted she travel alone to report the incident to Egypt's security forces, even though those same forces were implicated in the alleged crime.

"I was in a state of utter shock and terror," she said. "Already traumatised by being raped at a military checkpoint by a military official, and frightened about reporting it in a country under the control of the military, I was left on my own without any support or any sense that the consulate were sympathetic or willing to help."

The Foreign and Commonwealth Office has acknowledged that "aspects" of Tanya's complaint have been substantiated, prompting an internal review, local retraining and the updating of guidance given to diplomatic staff. But it denied that embassy officials failed to offer appropriate support at the time of the incident. "We have every sympathy with the victim of this particularly brutal attack," the FCO said. "Our consular staff in Cairo assisted her at the time and are following this case up with the Egyptian authorities."

Tanya was en route from Cairo to the Gaza border to take part in a pro-Palestinian demonstration in May when she became isolated from her companions and stuck at the military-run checkpoint in the Sinai desert. According to her testimony, which has been shared with the Guardian, she was forced into a small room by an officer and sexually assaulted, with her cries for help eliciting no response from nearby soldiers.

After getting away and making her way to the nearby city of Port Said, she made her first contact with the British embassy. What followed is a disputed sequence of events: Tanya claims that diplomatic staff declined to give her sufficient practical assistance and expressed little empathy with her situation, while the FCO insists that procedures were generally followed correctly – though it admits mistakes were made in the handling of the case.

Since the toppling of the former president, Hosni Mubarak, in February, the military has been in control of Egypt and maintained a tight hold over the security apparatus and the judicial system. Although some civilian police agencies have returned to work, they remain under the jurisdiction of the supreme council of the armed forces, a situation which made Tanya fearful of going to report her rape to the authorities without the protection of embassy staff.

But according to FCO correspondence, diplomatic officials "judged that [Tanya], with the assistance of [her] friends, would be able to navigate and negotiate the Egyptian system to make the necessary appointments and follow these up", adding that logistical problems such as the existence of a curfew and miscommunications complicated their ability to help.

Tanya went on to report the alleged assault to local police without any embassy staff present and was quickly directed towards the military prosecution office, where she says she was detained once again against her will.

"I had been raped by a military official, at a time when Egypt was under military rule," she said. "My friends and I were understandably very frightened about how we would be treated if I reported the crime to the authorities responsible for rape. It should have been obvious to the consular staff that offering to accompany me to report the crime was of utmost importance, and that this could not be delayed because of the short forensic evidence window."

Tanya believes the consular staff's handling of the situation "seriously undermined my ability to effectively pursue my right to an effective remedy in Egypt".

The status of the accused officer remains unknown, as investigations conducted by the military prosecution are often shrouded in secrecy. Tanya recently gave an Egyptian lawyer power of attorney, and the Cairo-based Egyptian Initiative for Personal Rights, a Cairo-based human rights organisation, is helping her pursue the case.

UK officials say they have sent note verbales – unsigned diplomatic communications – to the authorities in Egypt regarding the alleged crime and are planning to raise it with Egyptian defence staff directly.

After two investigations into their interactions with Tanya, the FCO has "committed to a series of improvements", including providing Cairo embassy staff with extra training on how to handle rape and sexual assault cases and working on improved relationships with the Egyptian military. It is also updating the global guidelines issued to staff on mistreatment and torture, after acknowledging that Tanya was a victim of the latter.

"Under international law, rape by a state official is clearly recognised as torture and is actually a very common form of torture," said Sarah Fulton, international legal officer at Redress, a London-based non-governmental organisation dedicated to helping torture survivors, which has taken up Tanya's case.

"Rape as torture has been under-reported and has generally gone unrecognised as a method of torture, but it's now very clearly recognised under international law," Fulton added.

"There's a traditional understanding of torture – a man on his own in a locked room being beaten – and even in that environment sexual assault is very common. But there's a growing recognition that torture goes beyond that particular situation, and in Tanya's case there was definitely a failure on the part of the FCO to recognise the context in which the rape took place and act accordingly."