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An Istanbul court issued the warrant, the first after the failed putsch for the reclusive cleric in Pennsylvania, the Anadolu news agency said.
In the warrant, Gulen stands accused of “ordering the July 15 coup”, Anadolu reported.
Gulen strongly denies any involvement and the movement he leads insists it is a charitable network promoting tolerant Islam.
Turkey previously issued an arrest warrant for Gulen in December 2014 on charges of setting up and directing an “armed terrorist organisation” as well as using intimidation to deprive a person of their freedom.
Ankara has frequently called on the United States to extradite Gulen, sending two sets of documents to Washington since the coup as evidence of his involvement in the putsch attempt.
Turkey has yet to make a formal extradition request to the US for Gulen.
A rogue faction within the military tried to wrest control of the country on July 15, launching attacks on parliament and the president’s palace.
At least 272 people including 34 coup plotters were killed and nearly 2,200 injured after people took to the streets and squares against the putschists.
Since then thousands have been purged from their roles in the judiciary, police, military and education system, accused of being members of the coup movement while more than 25,000 people have been detained.
Western allies including the EU have expressed concern over the purges, fearing a witch hunt and the possibility innocent people will be caught up in the government crackdown.
Gulen nephew arrested
Turkish media including CNN-Turk broadcaster reported that Gulen’s nephew, Muhammet Sait Gulen, was also arrested on Thursday in Ankara.
Gulen’s relative was detained on July 23 in Erzurum, eastern Turkey where his 75-year-old uncle is said to have developed his deep convictions, close to his birthplace of Korucuk.
He had been detained in connection with the coup and over the leak of questions from 2010 civil service exams, the latter which he admitted to, CNN-Turk reported.
He also denied being a member of the “Fethullah Terrorist Organisation”, the name Ankara gives to the movement it claims is running a parallel state.
The cleric and members of the movement deny these accusations.
Meanwhile, two members of Turkey’s top constitutional court were dismissed from the profession after they were arrested over alleged involvement in the coup attempt, Anadolu reported.
‘Tip of iceberg’
Earlier in the day, Erdogan said in a speech live from the presidential palace that businesses linked to Gulen would also come under scrutiny and would be cut off.
“At the moment, those captured are just the tip of the iceberg, others continue working. There is no doubt a pillar of this organisation is the business world. Perhaps that is where they are the strongest.
“We will cut off all their business links, all the revenues of Gulen-linked businesses,” Erdogan added in a speech to the heads of chambers of commerce in Ankara.
Erdogan said the Gulen “virus” spread everywhere and vowed to cleanse the state from the movement.
“Each school, each house, each cramming school and each company of this structure is a hotbed of terror,” he said.
“Those men are murderers … those men are hypocrites … those men are insidious … those men are thieves.”
More than 13,000 people have been remanded in custody while nearly 75,000 passports have been cancelled since the coup bid.
Over 60,000 people within military, judiciary, civil service and education have been dismissed, detained or are currently under investigation for suspected links to the Gulen movement.