
The case has drawn criticism from human right groups and the European Union.
Colonel Ali Oz was indicted last year for failing to provide protection to Hrant Dink, who had received death threats before he was murdered in Istanbul by a nationalist gunman.
A lower court dismissed the case against Oz but, on Tuesday, a court in the city of Trabzon said Oz should stand trial.
Two low-ranking soldiers are already on trial accused of neglect of duty in the Dink murder.
Dink received numerous death threats because of articles urging Turkey to accept responsibility for its part in the mass killings of Armenians by Ottoman Turks and Kurds in 1915 -- a highly sensitive issue for Turkey.
The EU, which Turkey aspires to join, has criticised Ankara for what it says are restrictions of freedom of expression.
Turkey's powerful military, once beyond prosecution, has come under increasing scrutiny following a wave of detentions and arrests that have targeted retired and army officers for allegedly planning a coup to topple the ruling AK Party.
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