The Foreign Office has been forced to apologise and pay compensation to a British woman who, after being raped by an Egyptian army officer, was left alone by embassy staff to seek medical treatment and to report the crime to the same authorities to whom her attacker belonged.

In a critical report, the parliamentary ombudsman pinpoints a series of "failures" by embassy staff on the ground and chided the Foreign Office for not being "open and accountable" and for not acting "fairly and proportionately".

"[The actions] were so poor that they were maladministrative," says the report, which adds that the young woman had suffered an "injustice".

The ombudsman found that, contrary to the Foreign Office's own guidance, embassy staff did not offer to accompany the woman to report the crime; help to arrange a medical examination immediately; help her to find a lawyer; and help her to understand she would require post-exposure prophylaxis – a treatment that can prevent HIV infection once the virus has entered the body.

The woman, a 35-year-old humanitarian worker living in Egypt, was sexually assaulted after being stopped at a security checkpoint near El Arish, on the Sinai peninsula. She contacted the British embassy in Cairo for help, but said diplomatic staff failed to offer any assistance.

She was forced to travel alone to report the incident to Egypt's security forces, even though those same forces were implicated in the crime. She ended up in a "chaotic" police station, where she had a "panic attack". She was then driven to military headquarters and questioned at gunpoint.

At the time of the rape, which was first highlighted by the Guardian, three months after the fall of Hosni Mubarak, a council of army generals governed Egypt and exercised tight control over the country's security apparatus. A curfew was in place. The embassy staff in Cairo said that as breaking the curfew was a criminal offence, they decided to handle the situation over the telephone instead.

However, the ombudsman dismissed this defence. "She had first contacted the FCO at 3.24pm on 15 May 2011 and the curfew in Cairo did not start until 2am the following morning. There was therefore no physical reason why a member of the embassy's consular staff could not have arranged to meet [her] immediately, or offered to accompany her to the hospital or to report the crime to the police straightaway".

The victim said she "would never trust a British embassy official again. I am pleased with the [ombudsman's] report but it does not go far enough. The Foreign Office failed to respond to a victim of sexual assault and a victim of torture. They did not identify me as being in their care, as vulnerable. They did not do anything for me".

An Egyptian government official, speaking on condition of anonymity, said the lieutenant concerned was tried, convicted and jailed – but would not disclose the length of his prison sentence.

The Foreign Office has apologised for the injustice the woman suffered and paid her £1,000 compensation for the way her complaint was handled.

The victim was supported by Redress, a charity which helps survivors of torture to obtain justice and reparation. Sarah Fulton, its international legal officer, said that initially the Foreign Office had been "very defensive" and it had taken two years of a parliamentary investigation to get it to admit culpability.

"The Foreign Office initially in January 2012 said with hindsight they could have handled it better. What the victim needed was a speedy, fair resolution of her complaint rather than fighting the civil service for two years."

Simon Fraser, permanent under-secretary and head of the diplomatic service, said: "We apologise unreservedly to Ms M for the mistakes we made in her case and fully accept the recommendations in the ombudsman's report. We have taken a number of actions to ensure that this does not happen again and we will give Ms M a comprehensive update on the steps we have taken in December."

As a result of the investigation the FCO has reviewed the way it handles complaints "so that the needs and feelings of the complainant are at the centre of the process. It has changed its guidance on consular assistance to take account of people's particular circumstances and changed its approach to complaint handling and training so that staff learn from mistakes".

Julie Mellor, the parliamentary ombudsman, said: "This is a prime example of how one individual coming forward to complain can lead to significant changes. Having the courage and persistence to seek justice can have an impact, not just for the individual, but for other people who may need to complain in future."

According to Egypt's interior ministry, 20,000 women are raped every year in Egypt, while the Egyptian Centre for Women's Rights estimates that the real figure may be 10 times higher. Campaigners say victims are often too ashamed to report sexual abuses, or afraid of how they will be treated by police officers – who sometimes harass women who dare to ask them to investigate sexual crimes.