"I have been watching this process closely as president of this country. Everything is lawful and in line with procedure ... A really diligent and clean process is going on at the moment," Erdogan said in a televised speech in Istanbul.
"The police and judiciary are not repeating the mistakes of the past," he added.
Erdogan defended the detention of journalists as part of the probe, saying that some journalists were using the profession as a "mask" for other activities.
His comments came a day after an Istanbul court issued an arrest warrant for the US-based Gulen, who Erdogan accuses of running a "parallel state" from his exile in the US state of Pennsylvania.
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A court yesterday also remanded in custody on terrorism charges the head of the pro-Gulen Samanyolu TV Hidayet Karaca and three others, although the editor-in-chief of the equally pro-Gulen Zaman newspaper Ekrem Dumanli was released.
The detention of 30 people last weekend on raids on journalists, scriptwriters and police deemed close to Gulen was sharply criticised by the EU, who in turn aroused Erdogan's own ire.
Erdogan's heated rhetoric against the EU adds to existing problems for the long-stalled membership bid of Turkey, already held up by disputes on Cyprus and human rights.