The EU is struggling to contain its worst foreign policy crisis in recent years after a whistleblower claimed that evidence of corruption in its biggest foreign mission – which is intended to strengthen the rule of law in Kosovo – was covered up.

The whistleblower, Maria Bamieh, learned in August that she would be made redundant from the Eulex mission, despite an impressive record of convictions, after revealing evidence of possible bribe-taking at top levels in the mission.

Bamieh, a British prosecutor, claimed her dismissal followed two years of unfair treatment, including full-scale investigations into her conduct for petty misdemeanours such as parking infringements.

Eulex has cost more than €1bn (£753m) since it was established in 2009 with a promise of pursuing the “big fish” among Kosovo politicians who are alleged to be involved in graft and organised crime.

Bamieh’s claims, along with the appearance of compromising documents in the Kosovan media, have reinforced a strong impression in parts of the former Yugoslav province that Eulex has become part of the problem rather than the solution.

During Eulex’s six-year tenure, analysts in Pristina say, corruption and organised crime in the political system since independence in 2008 has worsened.

After Bamieh complained about her dismissal to Brussels and the UK Foreign Office – and raised the corruption allegations once more – she was suspended and escorted out of the Eulex headquarters in Pristina on 24 October, for “gross misconduct”.

Eulex later said she was suspected of leaking classified documents. Bamieh denies the accusation, insisting she only went to the press after being suspended.

“It’s quite shameful that an organisation that is supposed to be a rule of law organisation is not itself subject to the rule of law,” Bamieh told the Guardian. “What message is that sending to Kosovo? You are telling Kosovo that if you have whistleblowers in your organisation, you kick them in the teeth. You are sending a message that we are not serious about corruption, that the institution that is here supposedly to raise legal standards is acting in this shameful way.”

The Eulex judge and prosecutor at the heart of the crisis deny any wrongdoing. Bamieh says there is no proof of illegal behaviour but maintains there is cause to launch an investigation.

Criticism in the European parliament has also focused more on the handling of the affair by the Eulex leadership than the original allegations, amid claims of a coverup. The organisation Reporters without Borders rebuked the mission for threatening a Kosovan journalist with prosecution in an attempt to stop him reporting on the scandal.

The recently-arrived new head of the Eulex mission, Gabriele Meucci, promised that Bamieh’s claims would be thoroughly investigated. “We are taking all allegations very seriously,” Meucci said last week, but he did not explain why it had taken a year to launch an internal inquiry and why it had yet to produce any visible results.

In what was widely seen as a vote of low confidence in the Eulex inquiry, the EU’s new foreign policy chief, Federica Mogherini, announced in Brussels this week that she would dispatch an independent legal expert to oversee its progress.

Richard Howitt, spokesman for the Socialist and Democrat group in the European parliament welcomed the decision, saying Eulex’s own investigation “looked more like a coverup”. Howitt added that Bamieh should have been offered legal protection as a whistleblower under Kosovo and EU law, which he said “clearly hadn’t been applied”.

Bamieh described Mogherini’s move as a step in the right direction. “I hope they send an independent expert. I don’t trust them to investigate themselves,” she said.

The appointment of an outside investigator reflects growing impatience with Eulex in Brussels. The Italian judge at the centre of the case, Francesco Florit, told the Guardian he had yet to be questioned by a Finnish investigator hired by Eulex to lead the internal inquiry. Eulex only announced last week, following Bamieh’s claims, that it had asked for Florit’s diplomatic immunity to be waived.

Florit said he welcomed that move as it would allow him to clear his name. He argued that the internal Eulex investigation should never have been launched on the basis of what he dismisses as groundless claims against him.

“What is unacceptable was that the previous head of mission established a mechanism that has spun out of control,” Florit said in an interview from his home in Italy. “He should have said: ‘This is rubbish and this stops here.’”

Bamieh, who formerly worked for the UK’s Crown Prosecution Service, first raised concerns about Florit and Jaroslava Novotna, Eulex’s chief prosecutor, after their names surfaced in a corruption case she was investigating in May 2012.

The permanent secretary at the Kosovo health ministry, Ilir Tolaj, had been arrested on suspicion of manipulating tenders for the supply of medicines to the advantage of himself and his friends.

However, Bamieh learned he had a mobile phone in his cell and ordered a wiretap on the number. In the resulting intercepts, people claiming to be intermediaries told Tolaj they had meetings with Florit and Novotna in which the officials suggested they could have Bamieh removed from the case and Tolaj freed.

In the transcript of a conversation on 31 May 2012, one of the go-betweens claimed Florit had described Bamieh as very difficult to deal with and promised to talk to her Czech boss, a reference to Novotna. According to the intercept, Florit is also alleged to have promised to “do everything to help [Tolaj] because he thinks that man deserves to be helped”.

In another conversation, an intermediary also portrayed Florit and Novotna as raising the possibility of replacing Bamieh with an Italian prosecutor on the Eulex staff. One of the intermediaries said if Florit “guarantees that the matter is done, he shall tell us … what can we do for him”.

Florit admits he met one of the alleged intermediaries recorded on the wiretaps, “maybe six or seven times” in 2012, but said the Kosovan presented himself as an academic asking him to attend lectures at a private Pristina university. Florit said there was a Kosovan assistant present at most of the meetings and that when his visitor raised the Tolaj case at their last encounter, in June 2012, he asked him to leave and wrote an official report about the visit. “It was my practice to allow anyone who wanted a meeting with me into my office, but I admit I was naïve in this case,” Florit said.

Novotna also denies any impropriety. Eulex said she was not available for interview but the Czech news website, Lidovky.cz quoted her as saying: “I met no charged persons nor anybody else over penal affairs and I took no steps to influence the investigation in any way.”

Tolaj was eventually acquitted of charges of trying to obstruct justice, which had been based on the intercepts. Bamieh concedes that she herself played down the weight of the allegations in her July 2012 indictment of Tolaj, writing: “It is not suggested that Mr Florit or Mrs Novotna were involved in the attempts to obstruct justice. It is highly likely that the individuals involved were feeding Mr Tolaj inaccurate false information for their own interests.”

Bamieh now says she was trying to protect colleagues from public scandal in the mistaken belief that an internal Eulex enquiry into the intercepts would be launched. Two months before issuing her Tolaj indictment, she had taken them to the head of the Eulex justice department, saying they appeared to show serious violations and asking that “Eulex properly investigates this for my safety, for the integrity of my investigation and for the public image of Eulex”.

“This is a political time bomb and Eulex needs to deal with this ASAP,” Bamieh wrote.

However, no action was taken on her warnings.

“They should have examined everything. They should have got the telephone records for Francesco [Florit], they should have got the telephone records for Jaroslava [Novotna]. They should have seized their records. They should have taken their diaries and they should have quietly and properly investigated, and if they were guilty, dealt with it,” Bamieh said. “Instead they punished me.”

She said she was angrily rebuked by both Brussels and senior officials in Pristina. A year later, her office received a complaint from the families of two convicts in a 2009 murder trial in which she had been prosecutor and Florit had been judge. The families claimed they had contributed to a €300,000 bribe to Florit, on the understanding he would acquit or significantly reduce the sentences of all three defendants in the trial, who were accused of planting a bomb in a Pristina cafe. But they claimed he had reneged on the deal and only acquitted one.

The brother of one of the convicted men, Flurim Asani, described a trip to the Albanian port of Durres in the summer of 2009 with a lawyer, ostensibly to discuss the bribe.

“I was interested to see if the lawyer was really going to meet Florit,” Asani told the Guardian in a Skype interview from his home in Germany. “He met him outside a restaurant at the port terminal, and I walked after them for about 100 metres until they got on a yacht, a modern expensive yacht. They were gone for four hours. On the way back to Pristina later, the lawyer told me everything was fine. He said Florit would charge €10,000 per defendant per year to reduce the sentences.”

Asked if he was sure it was Florit he had seen in Durres, Asani said: “I am absolutely certain. I had seen Florit 30 times at court hearings, and close up in his office when I would come to ask permission to visit my brother in prison.”

Florit dismissed Asani’s account as “an absurd lie”, saying he never been to Durres, and had not visited Albania in the whole of 2009. “I was never offered, and I never requested any kind of bribe,” the judge said.

Florit and Bamieh traded angry accusations on Kosovo television last week, further denting public faith in Eulex as a cure for Kosovo’s ingrained corruption problems.

Shpend Ahmeti, Pristina’s reformist mayor and a longstanding Eulex critic, said: “We want to discuss with Brussels how to replace Eulex with good local investigators and prosecution and the EU helps us with advice not in executive power … This is a problem of accountability. Eulex has no accountability to the Kosovo people.”