The ruling AK Party has frequently clashed with the secular military since sweeping to power in 2002, and this year’s round of promotions was fraught with tensions.

Chairing a promotion panel dominated by military top brass last week, Erdogan refused to sanction the commanders’ first choice to become army chief as the general they chose was one of 19 officers summoned by a state prosecutor to give testimony in an investigation into the anti-government slur campaign.

That meant the Supreme Military Council had to stall promoting the current army chief, General Isik Kosaner, to the top slot as chief of staff for the Turkish armed forces, the second largest in NATO. “We are not going to give the nod to everyone who comes our way,” Erdogan told reporters on Sunday evening after a compromise was reached. “We used the authority at our disposal.” On Monday, the military issued a statement announcing Kosaner would indeed succeed General Ilker Basbug as chief of staff.

The next commander of land forces, the head the army, will be General Erdal Ceylanoglu, who got the job after Erdogan blocked the favorite, General Hasan Igsiz, commander of the prestigious First Army.

Igsiz, who has been replaced as commander of the First Army, is not the only officer to be passed over during this year’s promotion round.

In a separate investigation, prosecutors have issued arrest warrants for 102 retired and serving officers in connection with a suspected coup plot in 2003 codenamed “Operation Sledgehammer.”

Eleven of these had been up for promotion, but were left kicking their heels due to the accusations against them.

The lack of consensus between the government and the military was cited as one cause of weakness in Turkish markets last week, as the country heads into a period of political uncertainty, with a referendum on constitutional reform looming on Sept. 12, and a general election due by July next year.

Erdogan is disliked in the military because of his radical past, though the ruling AK Party, which has pushed for Turkey to join the European Union depicts itself as akin to Europe’s conservative Christian Democrat parties.

The military sees itself as the guardian of secularism in Turkey, and has staged three coups between 1960 and 1980. It also forced the government to resign in 1997.

But reforms undertaken to bolster Turkey’s bid for EU membership have curbed its powers.

Kosaner, regarded as a staunch secularist, has not commented publicly on the “Sledgehammer” case, and any remarks by him will be closely scrutinized.

According to prosecutors, the “Sledgehammer” plot involved bombing mosques and triggering conflict with Greece in order to destabilize Erdogan’s government.

The military says “Sledgehammer” was an exercise presented at a war game seminar.

The case is due to go to trial in December.