Monday's arrests on charges of establishing an organised crime ring and inciting hatred based on ethnic differences increased suspicions that security forces may once again be attempting summary executions by death squads in their fight against Kurdish separatists.
The suspicions are troubling the government at the beginning of membership negotiations with the European Union.
Prime Minister Recep Tayyip Erdogan has promised "no cover-up" and vowed to shed light on the 9 November attack in the southeastern town of Semdinli.
The court on Monday charged and jailed paramilitary officers Ali Kaya and Ozcan Ildeniz in the city of Van, bordering Iran, after nearly 10 hours of questioning by a prosecutor and by the court, the Anatolia news agency said.
No verdict yet
Defence lawyer Vedat Gulsen said their arrests on Monday were a precaution, and should not be interpreted as a verdict.
"My clients have represented the institution that they belonged to with honour and they continue to do so," Anatolia quoted Gulsen as saying.
"My clients have represented the institution that they belonged to with honour and they continue to do so"
Defence lawyer Vedat Gulsen
General Yasar Buyukanit, the head of ground forces, said last week that the military high command did not order the bombing, but left open the possibility that soldiers may have been behind the attack.
The attack was on a Semdinli bookstore owned by Seferi Yilmaz, a former guerrilla who served 14 years in prison for participating in the Kurdistan Workers Party's (PKK) first and symbolic armed attack, in August 1984.
The group has been fighting for autonomy for Kurds in southeastern Turkey since 1984, and 37,000 people have died. It is considered a terrorist organisation by Turkey, the United States and the EU.
After the 9 November attack in Semdinli, in Hakkari province, bookstore owner Yilmaz and bystanders chased the suspected attacker, a former Kurdish separatist-turned-informant, to a car and captured him along with two paramilitary police officers standing nearby.
The informant and a sergeant who opened fired on the crowd at the scene have both been arrested.
The PKK has been fighting for
autonomy since 1984
Inside the car, allegedly owned by the paramilitary police, there were reportedly grenades similar to the one used in the attack, guns, plans of the shop and a list indicating which Kurdish clans were pro-state and which were not.
"The things that were seized in the car reveals everything," said Metin Tekce, the Kurdish mayor of Hakkari province.
A government report in 1998 admitted that Turkish officials had hired assassins and were involved in murders, kidnappings and bombings - many targeting Kurds in the early 1990s - confirming years of accusations by human rights groups.
There also have been recent claims that some security forces have engaged in violent operations to allegedly frame Kurds and provoke a military response against them, such as the 20 November grenade attack on a police station in Silopi that was initially blamed on Kurdish separatists.
Last week, two government-paid armed village guards - who fight alongside Turkish troops against the separatists - were arrested in connection with that attack.
The 1998 report grew out of an investigation into state links with organised crime after a scandalous traffic accident near the western town of Susurluk in which a police chief, a wanted hit man, a lawmaker and a beauty queen were riding in the same car.
Only the lawmaker survived and he is still on trial.
Several newspapers and Kurdish politicians have alleged similarities with the "Susurluk scandal" and the bombing in Semdinli which sparked days of rioting by Kurdish separatist sympathisers that left four people dead.