Turkey's government sparred with the military on Thursday amid tension over the trials of retired and active military officers and other alleged coup plotters, some of whom have been in jail for years.
This week, top prosecutors investigating the alleged plots by hardline secularists against the Islam-based government were replaced in what analysts saw as an effort to restore confidence in the judiciary's handling of the cases.
Hundreds of people, including military figures, academics and journalists, are accused of involvement in conspiracies to topple the government of Prime Minister Recep Tayyip Erdogan, which seeks a third term in elections in June.
Around 400 people, including some of Erdogan's fiercest critics, have been on trial since 2008, charged with terrorism offenses as part of an alleged anti-government network called Ergenekon. Oz accused them of trying to pave the way for a military takeover in 2003 through attacks designed to create chaos and trigger a military takeover.
Another 163 retired and active military officers were also jailed on suspicion of plotting a separate coup in a case known as Sledgehammer. The military, perpetrator of coups in the past, says the case is based on documents presented to a military seminar where scenarios of how to handle internal strife were discussed.
On Wednesday, the military criticized decisions to keep more than 100 active duty officers jailed pending the outcome of the trial, saying it could not understand the lengthy detentions. The statement on the military's website drew sharp rebukes from ruling party officials, who accused the armed forces of interfering with the independence of the judiciary.
"Court decisions may not be to everyone's liking," Huseyin Celik, a lawmaker with the Justice and Development Party, said Thursday. "However, if an armed organization reacts and makes an official statement, this amounts to interference in the judiciary."
Parliament Speaker Mehmet Ali Sahin made similar remarks, according to Turkey's Anatolia news agency.
Supporters of the coup plot trials hail them as a pillar of democratic reform, an opportunity to unveil an alleged network of armed extremists with links to the state who targeted perceived enemies over the decades. The cases highlight the gulf between the government, which has a strong electoral mandate, and opponents who alleged a government bid to muzzle dissent and undermine secular principles.
International observers initially welcomed the trials as a step toward transparency and accountability, but have grown increasingly uneasy at the long detentions of suspects without a verdict as well as concerns about freedom of expression in media reports on the cases.
The shakeup of prosecutors came after two investigative journalists, Ahmet Sik and Nedim Sener, were jailed for links to the Ergenekon. Turkish and international media groups denounced the arrests, and the West raised concerns about free expression in Turkey.
"There were so many flaws in the way the cases were being handled," said political commentator Cuneyt Ulsever. "The journalists' cases were the drops that caused the glass to overflow."
President Abdullah Gul, a close ally of Erdogan, has also expressed concern about how perceptions about the trials are hurting Turkey's image. Other government officials have acknowledged the trials are moving slowly, although they have also said the cases are a matter for the judiciary.
In such a highly charged political atmosphere, however, many analysts doubt the trials can be conducted entirely free of influence from Turkey's power structures.
In the judiciary's shakeup, lead prosecutor Zekeriya Oz, who had investigated the Ergenekon case from its inception several years, was transferred to the position of deputy chief prosecutor in Istanbul. Although a promotion, the new job effectively removes him from the coup plot investigations.
He was replaced Tuesday by Cihan Kansiz, a prosecutor who has led high-profile investigations, including that of the 2007 murder of ethnic Armenian journalist Hrant Dink, and prosecutions of leftist militants accused of terrorism.
Oz's deputy was also replaced.
Nihat Ali Ozcan, a political analyst at the Economic Policy Research Institute in Ankara, said Oz had become a polarizing figure but doubted that the new appointments would lead to a significant change in the course of the trials.
"The foundations have already been laid by Oz," he said.
Associated Press reporter Selcan Hacaoglu contributed to the report.