The final in Julian Borger’s series on Kosovo explores how senior figures in the governing party are being targeted in a major Eulex inquiry

The EU legal mission in Kosovo, under fire for allegedly shielding powerful local politicians, reopened an investigation on Friday into connections between a convicted hit-man and senior figures in the governing party.

The move comes at a time when the EU is to send a legal expert to scrutinise the operations of the EU Rule of Law mission in Kosovo, Eulex, which is in crisis following recent allegations by a British whistleblower that it has been covering up evidence of corruption.

The investigation has been launched five years after a confessed assassin, Nazim Bllaca, claimed on video to have taken part in numerous killings of political opponents as part of a hit squad working for the intelligence wing of the governing PDK party.

A new investigation into the shadowy spy group, known as Shik, could also prove embarrassing for western intelligence agencies, particularly the CIA and France’s DGSE, whose support for prime minister Hashim Thaçi, the PDK and Shik dates back to the 1998-9 Kosovo war. At the time, the Americans and French backed Thaçi as the most effective Kosovo Liberation Army (KLA) commander fighting the Serbian military, which was conducting a brutal counter-insurgency and “ethnic-cleansing campaign”.

Some Kosovar and Eulex investigators believe these wartime intelligence ties have helped protect the PDK leadership and held back efforts since Kosovo’s 2008 independence to curb the country’s runaway corruption and organised crime.

In his November 2009 video confession, Bllaca said he worked for Azem Syla, a former defence minister and several other powerful party figures.

According to the Kosovan daily Koha Ditore – which first published the revelations of the British whistleblower, Maria Bamieh, and the news of the Syla investigation – Bllaca’s family were moved abroad for their protection on Wednesday. The Guardian independently confirmed the launch of the Syla investigation with a Eulex source in Kosovo.

Syla and Thaçi have repeatedly dismissed allegations they were involved in corruption or political killings. Syla told Koha Ditore: “The credibility of such accusations is often unfounded and tendentious.”

In 2012 Syla was expelled from Switzerland, in part for abuse of the social security system, drawing €350,000 in disability payments there while he was working as a politician in Kosovo.

A Eulex spokeswoman, Dragana Nikolić-Solomon, said she could not confirm or deny an investigation was under way. “As you will appreciate, investigations cannot be commented in public. One of the main principles in such proceedings is the principle of confidentiality.”

The launch of the new enquiry, which will be conducted by Kosovan and Eulex investigators, will raise questions of why it was not begun five years earlier.

In his 2009 video Bllaca said that he worked for the execution arm of Shik, charged with killing “collaborators”, LDK officials and potential witnesses against KLA commanders for war crimes.

He said that between 1999 and 2003 he took part in an estimated 17 crimes, including assassinations, attempted assassinations, threats and blackmail, claiming that he worked directly for Syla.

His explosive testimony threatened to devastate the PDK and confirm suspicions that Shik, supposed to have been disbanded, remained a potent force in the shadows of Kosovan public life.

According to Andrea Capussela, former head of the economics unit in the International Civilian Office, a multilateral supervisory body in Kosovo, Shik is “the elite’s main instrument for political crime and a major criminal enterprise in its own right, with estimated annual earnings of $200m (£125m).”

Bllaca’s confession was highly embarrassing for Eulex as it turned out he had attempted months earlier to give his testimony to a top European prosecutor from the mission, who did not make a record of it. Furthermore, it took four days from Bllaca’s public testimony for Eulex to arrest him and put him in protective custody.

Bamieh, the British whistleblower at the heart of the current Eulex crisis, told the Guardian that she was prevented by a more senior prosecutor from questioning Bllaca about his information on PDK leaders and their involvement in suspicious privatisation deals. Bamieh was told he was not a credible witness.

“Evidently … his statements were judged credible in the parts in which he incriminated himself and other killers like him, but not credible in the parts in which he accused members of the political elite, despite the fact that such statements exposed him to a high risk of retaliation and were therefore unlikely to be knowingly false,” Capussela said in an assessment of Eulex’s six years of operations.

The new spotlight on the campaign of assassinations by Shik, may also prove uncomfortable for western intelligence agencies which helped set up the organisation during the Kosovo war, in which Nato sided with the KLA to oust Serbian forces from the former Yugoslav province, paving the way for its declaration of independence in 2008.

Kadri Veseli, the Shik chief and a close aide to Thaci, told the US news website GlobalPost in 2011: “We had a lot of partners — 25 intelligence services … The US, they help us a lot.”

Veseli said foreign intelligence services helped Shik “in every way”, but denied that Shik had carried out systematic political killings.

As well as the CIA, Shik received particular support from France’s external intelligence service, the DGSE. France, alone among the western allies, had provided military training for the KLA. British wartime intercepts of Serbian military communications during the Kosovo war, even revealed that DGSE officers had been killed alongside KLA fighters in a Serbian ambush.

In the spring of 1999, according to investigators who have tracked Shik’s activities, a group of 20 Shik recruits were taken out on a boat from the Albanian port of Durres and transferred to a French warship. They had been dressed in dark blue shirts so they would blend in with the French soldiers. Shipped to France they were given specialist weapons training as part of what was supposed to be a course in close protection. But according to investigators, some of the French-trained Shik recruits later became members of the assassination squad.

The French connection with Shik was strengthened when French troops took over control of northern Kosovo after the 1999 Nato intervention, which included the Drenica region, home to Thaci’s family and his close circle. A former head of DGSE operations, Xavier Bout de Marnhac, ran Eulex from 2010 to 2012.

A Kosovan investigator estimated the hit squad was responsible for as many as 30 killings, and that the French connection had helped played a part in Eulex’s apparent reluctance to pursue investigations to the top reaches of Kosovan politics.

“These shooters are not important in themselves, but they are linked to protected people,” the investigator said. “People from different countries have an emotional bond from the war.”

“It is true that in late ‘99, French contacts were closer to the PDK and Shik since French troops were deployed in areas where this group was stronger,” said a former French official who served in Kosovo. “But the ‘cooperation’ never went as far as what is told now by some people. And the US went far beyond! It is true that France trained some people, but it was within the framework of the creation of the Kosovo Protection Force.”

The western agencies seconded officials to the Central Intelligence Unit (CIU) in Unmik, the UN mission which ran Kosovo between the war and independence. After a string of police arrests of suspects with Shik connections in 2004, the CIU insisted on a ‘flagging’ system, in which Kosovan police had to give it prior notice of investigations and detentions. This, the investigator said, had the aim of protecting agents and wartime allies.

In 2008, the CIU database was supposed to be passed on to the incoming Eulex mission, but it was destroyed in an unexplained fire while being store at a Nato base in Pristina.

This article was amended on 9 November 2014 while an element of the story is pending investigation.