The European Union’s €1bn flagship foreign mission to combat organised crime and corruption in Kosovo repeatedly shunned or dropped investigations of cases implicating senior Kosovan politicians, according to a new study of the mission’s six-year existence.

The findings have emerged as the EU rule of law mission, known as Eulex, is already under scrutiny for the alleged cover-up of corruption allegations within its own ranks.

The new EU foreign policy chief, Federica Mogherini, has promised to send an independent investigator to Kosovo after a whistleblower alleged that evidence of possible bribe-taking had been ignored for more than a year.

An analysis in a forthcoming book by Andrea Capussela, head of the economic unit in the international mission that supervised Kosovo after independence, suggests the current scandal is only a small part of much broader problems in the troubled mission.

Eulex was set up in late 2008, in the wake of Kosovo’s independence, to mentor and monitor its fledgling judicial system, but it has had extensive executive powers to investigate, prosecute and judge important cases involving war crimes, organised crime and corruption.

Capussela analysed the 15 significant cases in which Eulex had issued indictments, of which four led to convictions, an average of 2.5 indictments and one major conviction per year.

“Considering how widespread political corruption and organised crime are in Kosovo, these results are gravely inadequate,” Capussela said, arguing that the mission had “disregarded its mandate”.

In eight known cases, in which Capussela says there was “credible and well-documented evidence strongly suggesting that serious crimes had been committed”, Eulex issued no indictments or carried out no investigations at all.

He suggests there are likely to be many more unexplored cases which have left no official traces whatsoever. Eulex, for example, inherited 1,187 cases from the UN mission in pre-independence Kosovo, Unmik.

Of the 15 major cases where Eulex did issue indictments, Capussela argues that seven were forced on it by outside pressure. Either the mission became aware that its inaction was about to be exposed, or “after EU or international public opinion demanded an investigation”.

In three out of the four cases where convictions were achieved, they involved secondary figures. Higher-ranking figures linked to the same crimes were either not investigated or indicted, Capussela says in his book, State-building in Kosovo: Democracy, EU Interests and US Influence in the Balkans, due to be published in February.

“Eulex’s conduct in these 15 cases – the eight ignored ones and the seven opened under pressure – suggests that the mission tended not to prosecute high-level crime, and, when it had to, it sought not to indict or convict prominent figures,” he said.

“The passivity exhibited by Eulex has confirmed the apparent sacrosanctity of the elite instead, and it has reinforced what has aptly been called Kosovo’s “glass ceiling of accountability”. As a result, he said a number of indicators suggested that corruption and organised crime had actually worsened under Eulex’s tenure.

A senior Kosovan investigator agreed with Capussela’s conclusions. Speaking on condition of anonymity he said his investigations involving senior figures in government had repeatedly hit a dead end in the international institutions supposed to be bringing the rule of law to the country.

“There are people killing people and getting away with it because of Unmik and Eulex,” the he said. He added that Eulex’s performance was worse than Unmik’s, because its leadership had grown so close to the government of prime minister Hashim Thaci.

“The political elite and Eulex have fused. They are indivisible. The laws are just for poor people,” he said.

Capussela explains the failure to confront Kosovo’s leadership is in part because of a mismanagement of resources which left the mission short of prosecutors in critical areas. More fundamentally, he said Eulex was supposed to be two things at once: a political mission attempting to keep the peace and build better relations with Serbia, and a judicial mission, meant to lock criminals away.

“The management found it hard to antagonise the elite,” he said. “You can’t talk to a minister one day and send him to jail the next day.”

Capussela said he sent a manuscript of his analysis to Eulex for comment but received no response. But a spokeswoman for Eulex told the Guardian that while Capussela may have used his own criteria for what constituted an important case, “we believe that every case we have prosecuted is important, and especially so to the victims or their survivors”.

The spokeswoman said Eulex special prosecutors “work on the most serious cases – war crimes, terrorism, trafficking in persons, corruption, organised crime, etc. The mission has obtained 20 verdicts in the fields of organised crime, trafficking in human beings and trafficking in human organs and 43 verdicts in the field of anti-corruption, such as fraud, accepting or giving bribes, abusing official positions. We’ve obtained 30 verdicts in the field of war crimes, including several cases of conflict-related sexual violence.”

There is growing disillusion within Kosovo with Eulex’s performance. When the mission arrived, promising to go after the “big fish” in the nexus of organised crime and politics that had a stranglehold on Kosovo, it was met with euphoria. There was even a petition to have a street in central Pristina renamed in honour of its acting chief prosecutor. Last week, after cover-up allegations by the British Eulex prosecutor, Maria Bamieh, protesters from the opposition party Vetevendosje staged a demonstration outside Eulex HQ mocking its earlier promises, holding fishing rods with copies of €50 notes attached as “bait”.

“Eulex came here to build law and order and they got domesticated,” said Ilir Deda, a Vetevendosje MP.

“It is incredible they managed to fail in a society that was so pro-western, was so pro-democracy. But corruption has grown exponentially under the eye of Eulex. We have made so many steps backwards.”

Deda says he has long experience of western failure to curb corruption. He was an adviser in a pre-independence Kosovo government in 2004 when he became aware of corruption by senior officials in the prime minister’s office.

He took his concerns to the Unmik, but there was no investigation. Instead he was advised to leave the country for his own safety as his complaint had leaked.

He spent a year in Switzerland, frequently changing addresses because of threats. “It took me years to recover and get over the bitterness,” Deda said.

Soren Jessen-Petersen, who was head of Unmik in 2004-06, and made efforts to make it more aggressive in its approach to high-level crimes, said he constantly ran into resistance from western capitals seeking to protect their own partners and allies among Kosovo’s leaders.

He said he would get calls from senior western officials seeking to dissuade him from high-profile operations.

“In mid 2005, following months of investigation into suspicions of corruption and organised crime among the staff of a high level Kosovar politician, Unmik had engaged in careful planning together with K-For [the Nato force in Kosovo] for an early morning raid into the concerned offices to confiscate relevant documentation,” Jessen-Petersen recalled in an email to the Guardian.

“Just a few hours before the start of the operation I received a call from Nato that important member states had objected to the operation, deemed too risky, and that Nato therefore had to withdraw.

“We had no choice but to call off the operation since going ahead without the necessary security back-up was not an option. We pursued the investigation in other ways but we were never able to gather credible evidence to pursue the cases in court.”

Jessen-Petersen said that in the circumstances the claim that the operation was “too risky” was not credible.

The most complex and sensitive case facing the international community in Kosovo, involving war crimes against Serbs, including some alleged cases of executions of Serb soldiers so their organs could be removed and sold for transplant, was taken out of Eulex’s hands entirely. In 2011, because of concerns that witnesses were not being given sufficient protection by Eulex, the EU set up a special investigative taskforce based in Brussels.

The chief investigator, Clint Williamson announced in July that there was evidence to indict senior Kosovan politicians for crimes against humanity, including killings, abductions, sexual violence and other abuses of Serb and Roma minorities.

But indictments can only be issued once a special new court is established, probably in The Hague. That cannot happen without constitutional changes approved by Kosovo’s parliament, and that approval in turn has been held hostage to political deadlock following elections in June.