Istanbul prosecutors launched an investigation into the Hurriyet front page story on Saturday which suggested that the army was not satisfied with the recent actions by the government.
The story listed seven grievances including the lifting of a historic ban on female officers wearing the Islamic headscarf in the officially secular country.
"Let me put it very clearly, what's done here, the headline they have used is insolent," Erdogan told reporters at an Istanbul airport before leaving for Pakistan on an official visit.
"No offence but I don't find such an approach forgivable at a time when we need unity, fraternity and solidarity more than ever," he added.
Erdogan said he discussed the issue with Chief of Staff General Hulusi Akar yesterday.
The government increased control over the armed forces in the wake of an attempted coup in July last year blamed on followers of preacher Fethullah Gulen.
The Hurriyet newspaper, the flagship daily of Dogan Media Group -- the Turkish media giant which owns television channels Kanal D and CNN-Turk -- is a mainstream daily but houses pro-government columnists as well.
Firat, one of Turkey's most prominent journalists, was fiercely condemned by pro-government media for "coup mongering".
Ironically, Firat played a crucial role in defeating the July 15 coup when she spoke to Erdogan live on her CNN-Turk show by FaceTime on the night of the putsch.
Erdogan used the interview to rally his supporters, calling them into the streets to resist the attempted power-grab.
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