A statement from the Istanbul state prosecutor's office about secret links between Kurdish separatists and security officials coincided with police raids across the country to detain around 100 people over alleged ties to Kurdistan Workers Party (PKK) militants in the same investigation.
The arrests came less than a week after prosecutors asked the head of the National Intelligence Agency (MIT) and his predecessor to testify over secret links between the PKK and the agency, controlled by Prime Minister Tayyip Erdogan.
The government has moved to block the questioning of MIT operatives with a parliamentary bill requiring Erdogan's permission for such a move. At the weekend the prosecutor who ordered their questioning was removed from the case.
However, Istanbul deputy chief prosecutor Fikret Secen said in a written statement defending the investigation that it was only directed at the actions of individual officials and not against government anti-terrorism policy.
"This investigation ... was launched due to evidence giving rise to suspicion that some state officials acted outside the duty given to them by the executive organ and aided the [militant] organisation in executing its operations," it said.
The head of MIT, Hakan Fidan, is close to Erdogan and the current probe is seen as exposing tensions between his organisation and elements within the police and judiciary.
Istanbul prosecutors have asked their Ankara counterparts to summon Fidan, while detaining four other MIT officers for questioning but no action has been taken so far.
The prosecutor's investigation is focused on an organisation called the Union of Kurdistan Communities (KCK), which the PKK is alleged to have established with the aim of creating its own political system in the mainly Kurdish southeast of Turkey.
Around 150 politicians and activists are already being tried in the region's main city of Diyarbakir on charges of membership of an armed terrorist group and hundreds more people have been detained in related cases.
SECRET OSLO TALKS
Security sources said those held on Monday were believed to be involved in bomb attacks and illegal protests and noted their detention came just two days before the 15 February anniversary of jailed PKK leader Abdullah Ocalan's capture in 1999.
The PKK, branded a terrorist organisation by Ankara, the EU and the United States, took up arms against the state in 1984 and more than 40,000 people have been killed in the conflict.
Prosecutors are also believed to want to question MIT officials about secret talks they held in Oslo with PKK representatives. The contacts came to light last year through recordings on the Internet.
Some have interpreted the targeting of the MIT as a nationalist warning to Erdogan against seeking any negotiated settlement with the PKK. Erdogan is currently recovering from his second bout of intestinal surgery in three months.
Talks between the state and the PKK were halted after Erdogan's AK Party won a third term in office last June with around 50 per cent of the votes. The PKK has returned to fighting using northern Iraq as a refuge for operations in south-eastern Turkey.
Erdogan, who has Islamist roots but whose AK party includes centre-right and even strongly nationalist elements, has pressed reforms in Turkey that have shaken the political establishment since he was first elected in 2002. He has cut back the influence of the army and shaken up a conservative judiciary.
In a country rife with conspiracy theories, some have also suggested that an influential Islamic movement, headed by Fethullah Gulen, a Muslim theologian living in the United States, could be seeking to clip Erdogan's wings.