One of Turkey's most powerful generals has been accused of setting up rogue units in the south-east of the country to provoke clashes between Kurdish separatists and security forces. The accusations, made by a prosecutor in the eastern city of Van, against General Yasar Buyukanit, the head of Turkey's land forces, have rattled the politically powerful military. It is thought the alleged activities are part of an effort to derail Turkey's bid to join the European Union.

General Buyukanit , who was chief commander in the region from 1997-2000, is due to become chief of staff in August. The separatist Kurdistan Workers Party (PKK) launched an armed struggle for a homeland in the region in 1984. The conflict has claimed more than 30,000 lives.

The charges were part of an indictment of two soldiers and a Kurdish informer over the bombing of a bookshop in November in the south-eastern town of Semdinli, on the Iraqi border. The general cannot be prosecuted by civil courts.

The blast, which killed one man, made headlines when a tale was revealed of shadowy rogue elements within the security forces. Local people chased and caught three men suspected of planting the bomb only to find out that two were non-commissioned officers, part of a paramilitary intelligence unit, and the third, a Kurdish rebel turned informer. Their car was registered to the local gendarmerie and contained a list of 105 potential targets, including the bookshop owner.

In his 100-page indictment of the three suspected bombers, a prosecutor, Ferhat Sarikaya, reportedly accused General Buyukanit and other senior officers of setting up an illegal force to create unrest among the Kurds that would undermine Turkey's application to join the EU. Mr Sarikaya alleged that the bombing in November was part of a series of similar attacks intended to provoke the security forces into a clampdown on the restive Kurdish region that would then unleash European criticism and jeopardise Turkey's hopes of joining the EU.

Turkey's army says it backs Ankara's mission to join the EU, but some officers fear that EU-required reforms would reduce the armed forces' influence, encourage Kurdish separatism and strengthen the Islamist movement.

For many, the Semdinli bombing brought back memories of the 1990s - the peak years of the conflict - when rogue elements in the security forces were accused of summary executions, extortion and kidnappings. Turks refer to those elements as a hidden "deep state". That murky era has yet to be investigated. General Buyukanit said last year that one of the three suspects, who had served under him, was "a good chap". In the indictment, General Buyukanit was accused of seeking to influence the judiciary by supporting the suspect. The three may be jailed for life if convicted.

Turkey's generals are widely seen as guardians of the pro-Western, secular system introduced by the founder of modern Turkey, Kemal Ataturk. Their powers have been scaled back recently in keeping with EU reforms, but the military still has influence over domestic and foreign policy.

Under Turkish law, members of the armed forces cannot be tried in civilian courts. General Buyukanit and other officers could only be tried if a military prosecutor decided to take up the investigation. The general staff has accused the Van prosecutor of overstepping the limits of his authority.