The high command of the Turkish armed forces has demanded a retrial for dozens of military officers convicted of plotting to topple the government.
A statement from the general staff, quoted by Turkish media, accused the judiciary and police of manipulation and fabricating evidence.
The legal complaint concerns two high-profile investigations, called Sledgehammer and Ergenekon.
The cases were seen as a challenge to modern Turkey's secularist traditions.
The former armed forces chief, Gen Ilker Basbug, was among dozens of people given long jail terms last August for involvement in the so-called Ergenekon plot.
Lawyers, politicians and journalists were convicted, along with many military officers.
Thursday's armed forces statement, quoted by the Hurriyet daily, said that "police officers, prosecutors and judges in the trials... ignored the pleas of defence lawyers and manipulated criminal evidence".
Two days ago opposition parties called for a retrial of the cases, after a key adviser to Prime Minister Recep Tayyip Erdogan, Yalcin Akdogan, spoke of a "plot" targeting the army and other institutions.
In recent days political tensions have been running high over alleged corruption in the Turkish government.
The ruling AK Party is rooted in Islam and has moved to curb the power of the Turkish military, which sees itself as guardian of the modern secular state founded by Mustafa Kemal Ataturk.
Three ministers resigned after their sons were arrested, along with dozens of others, over alleged wrongdoing in construction contracts and deals with Iran.
The controversy also led to dismissals of police officers and judicial officials. Mr Erdogan called the allegations a "dark plot" by destructive forces outside Turkey.
Analysts say the latest dispute is part of a power struggle between Mr Erdogan's government and an influential US-based Muslim cleric, Fethullah Gulen, who is said to have many followers within Turkey's police and judiciary.