By Ece Toksabay and Tuvan Gumrukcu
ANKARA/ISTANBUL (Reuters) - Turkey will soon complete an overhaul of its intelligence agency and make new appointments to its gendarmerie as it tries to rid its security apparatus of the followers of a U.S.-based cleric blamed for an attempted coup, officials said on Wednesday.
President Tayyip Erdogan said new appointments in the gendarmerie, responsible for security in rural areas and key in the fight against Kurdish militants, would come within 48 hours. Interior Minister Efkan Ala said work on restructuring the MIT intelligence agency was ongoing and "should not take too long".
More than 60,000 people in the military, judiciary, civil service and education have been detained, suspended or placed under investigation following the July 15 coup attempt, prompting fears among Western allies and rights groups that Erdogan is using the events to crack down on dissent.
The government says the purges are justified by the gravity of the threat to the state. More than 230 people were killed in the attempted putsch and parliament was bombed by the country's own aircraft and tanks for the first time in its history.
In a speech to the Religious Affairs Directorate, the country's top religious authority, Erdogan said he had initially misread the intentions of cleric Fethullah Gulen, whose network of followers were at one time close to his ruling AK Party.
"We did not see this structure had insidious plans," Erdogan said, dismissing Gulen as the "charlatan in Pennsylvania", where he has lived in self-imposed exile since 1999.
"I am very saddened by the fact that we were unable to see the true face of this cruel group before ... May my people and God forgive me," he said.
Mehmet Gormez, Turkey's top cleric, said Gulen's movement should not be seen as a religious community, describing it as a terrorist organization and saying it was "our moral duty" to stand against such structures.
"An organization that can massacre innocent people in one night cannot be associated with Islam," he said.
In interviews from his retreat in the Poconos mountains, Gulen has condemned the coup and denied any involvement. The 75-year-old preaches Sunni Islam together with a message of interfaith dialogue and has built a worldwide network of schools and institutions over several decades.
After their rise to power in 2002, the Islamist-rooted AKP founded by Erdogan became dependent on the Gulenists in their common fight against the army, which had long seen itself as guardian of the secular order.
It was mainly Gulenist prosecutors who, after Erdogan and his party narrowly escaped being banned in 2008, built two big conspiracy trials targeting the upper echelons of the military.
The purges of Gulen's suspected followers extended to the Scientific and Technological Research Council of Turkey (Tubitak), which saw its offices raided on Sunday, an official there said. Broadcaster NTV said "many people" had been detained, but the official gave no details.
Tubitak funds science research projects in universities and the private sector and employs more than 1,500 researchers, according to its website.
In the first visit to Turkey of a high-profile European official since the coup, the head of human rights body the Council of Europe said Turkey needed to take on those responsible for the putsch but stressed that this needed to be done in line with the rule of law.
Secretary-General Thorbjorn Jagland also said that there had been little understanding in Europe on the extent to which "this secret network" had infiltrated the army and judiciary, posing a challenge to Turkey's democratic institutions.
"The coup attempt was outrageous ... Last time there was a coup in Turkey, its membership at the European Council was suspended. If the coup makers had won that very night, the same would have happened, I am quite sure," he said.
"We see a need for cleaning all this up. (It is) important that this is done in conformity with the rule of law and human rights," he told a joint news conference with Turkish Foreign Minister Mevlut Cavusoglu in Ankara.
Erdogan and many Turks have been frustrated by U.S. and European criticism of the crackdown that has followed the coup, accusing the West of greater concern about the rights of the plotters than the gravity of the threat to a NATO member state.
Erdogan has issued two decrees dismissing around 3,000 members of NATO's second-biggest armed forces since the coup, including more than 40 percent of generals. He has also shut down military high schools and brought force commanders under tighter government control.
(Additional reporting by Humeyra Pamuk and Can Sezer, Ercan Gurses and Gulsen Solaker in Ankara; Writing by Nick Tattersall; editing by Philippa Fletcher)