Prime Minister Binali Yildirim was speaking during a televised interview on Tuesday evening.
When asked if an upcoming statutory decree will include structural changes to the Turkey's National Intelligence Agency – MIT – Yildirim confirmed there was “an ongoing study” with the organization.
"There is clearly a disorder about the intelligence service," Yildirim said, adding that Turkey's security department and gendarmerie also have intelligence units.
"If you don't have the intelligence, then you cannot take preventative measures," the premier said.
"The intelligence restructuring that we are working on right now will include lots of measures, including the handling of threats that come from inside and outside with the same level and will effectively make operations for it," he added.
Asked if the intelligence restructuring will be under MIT or another unit above it, Yildirim said teams assigned for the job "are working with a variety of options".
"Some countries keep foreign intelligence and domestic intelligence separate. Some countries bring them all under one roof. There are many options in the world. We will continue with our good habits and lose the bad ones," he said.
Yildirim also talked about the latest assignments of commanders, confirming that every newly-assigned general will start their duty before the weekend, aiming "not to leave any security weaknesses within the ongoing operations".
He added that President Recep Tayyip Erdogan will visit the General Staff on Wednesday.
Under a statutory decree, seen as part of the Turkey's current three-month state of emergency, military personnel found to be national security threats as well as members of the Fetullah Terrorist Organization (FETO), or linked to FETO, were expelled from the army.
Under the decree, Turkey's land, naval and air forces are now directly answerable to the Defense Ministry.
The decree also closes all of Turkey’s war academies, military high schools and high schools that train non-commissioned officers, to be replaced by a new college called the National Defense University under the Defense Ministry.
When asked if he had demanded an explanation from the intelligence agency as to why it was late to inform the president and prime minister about the coup bid, Yildirim said he had asked Hakan Fidan, chief of the intelligence agency, "but could not get an answer".
"He could not answer me, he was not able to say anything," Yildirim added.
Yildirim was asked whether he wants to continue with Fidan, he replied: "There are things which come first".
"We will do our self-criticism when we finish our part of taking measures after the coup bid," Yildirim said. "We will look back and criticize ourselves where we did wrong, where the bureaucracy did wrong.
"This was a huge crisis that we averted. Fighting and blaming each other will not help defeating the results of the crisis. On the contrary, your morale will go low," Yildirim added.
‘Executing with prejudice not for us’
When asked about whether innocent people could also be tried amid FETO-linked suspects, Yildirim said there may be some examples of this but "all the details are being investigated and all the options are being considered".
"Executing people with prejudice is not for us," Yildirim said. "The coup-plotters will not get away with what they have done. I would like to stress that [we] will act fairly. Because Turkey is a state of law and there is no room for terminating with prejudice in states of law."
The prime minister said if there had been some misjudgments made among suspended personnel, their objections will be considered.
"We set out some criteria. All of the people who have direct links with [FETO], who continued to support them financially after Dec. 2013 and people who have active roles in their organizations are taken into custody," Yildirim said.
The premier added that a total of 62,010 people had been suspended from duty after the failed coup bid but stressed that only 3,499 among those suspensions ended in dismissal.
"We dismissed the people who actively took role in the coup bid, who are traitors who wore military uniforms," Yildirim said.
U.S. based preacher Fetullah Gulen is accused of a long-running campaign to overthrow the state through the infiltration of Turkish institutions, particularly the military, police and judiciary, forming what is commonly known as the parallel state.
At least 238 people, including civilians and security personnel, were martyred – and nearly 2,200 injured – during the putsch attempt.