"The president has approved the assignment of military police chief General Necdet Ozel as the land forces commander. General Ozel is deployed as acting chief-of-staff," the president and prime minister's offices said in a joint statement.
The military police chief of the country was named acting chief-of-staff and the commander of land forces late Friday, in a quick move to contain the crisis.
Turkish President Abdullah Gul, commander-in-chief under the constitution, met with Prime Minister Recep Tayyip Erdogan and Ozel on Friday evening, leading analysts to speculate that Ozel was likely to become the new military chief.
According to previous army practice, an officer should serve as commander of land forces before becoming chief-of-staff, and Ozel is expected to be permanently assigned as chief-of-staff on Sunday, local media said.
Gul on Saturday insisted that Turkey was not in a crisis over the resignations. "There is no crisis," Gul said in his televised remarks. "Without doubt, what we went through yesterday was an extraordinary situation. But everything is now on course and normal procedures will go on," he said.
Turkey's entire military command, including chief-of-staff General Isik Kosaner and the commanders of the army, air force and navy resigned Friday in a row with the government over generals jailed for an alleged coup plot.
Kosaner stepped down after several meetings with Erdogan in recent days ahead of an early August meeting of the army's high command which decides on promotions for senior officers.
Media reports blamed tensions between the military and Erdogan over army demands for the promotion of dozens of officers being held on suspicion of involvement in an alleged anti-government plot.
"Mr. Kosaner is a valuable commander. He had been thinking of leaving the office for a while. Despite us wishing him to stay, we respected his decision," Gul said.
Kosaner was appointed to his post for a three-year term last year.
Forty-two generals and dozens of officers are in jail in a probe of alleged plots to unseat the government led by the Justice and Development Party (AKP), the moderate offshoot of a banned Islamist movement.
Earlier Friday, prosecutors indicted and asked for the arrest of six more generals for attempting to overthrow the government and launching websites for anti-government propaganda, media reports said.
The generals included Nusret Tasdeler, the commander of the Aegean army, Ismail Hakki Pekin, the head of army intelligence, and Hifzi Cubuklu, the military's judicial advisor.
The latest arrest warrants were the last straw for the top commanders, media reports said.
"One of the aims of those probes and long-standing arrests is to keep the army on the agenda and give the public the impression that it is a criminal organisation," Kosaner said in a farewell message to army members, Anatolia news agency reported.
Kosaner also accused the media of fabricating news and "encouraging the nation to take a stand against the army."
"As this situation cannot be prevented and applications to the authorities (for a solution) are disregarded, I, as chief-of-staff was not able to protect my personnel's rights," Kosaner said.
Several of the arrested soldiers are retired, but senior officers in the army have been trying to get some of the serving officers promoted despite their incarceration.
The government insists the group be forced to retire.