The documents published this week by the daily Taraf detailed the blacklisting of citizens and a 2004 plot against a prominent Islamic scholar.
Erdogan, speaking at a rally of supporters in Tekirdag, said the spilling of state secrets was specifically illegal under Turkey's Constitution.
"I now see that some media groups are hand-in-hand," he said. "Exposing state secret is not freedom but absolutely treason to the country and homeland."
Today's Zaman said Saturday the leaks prompted the filing of complaints by Erdogan's office and two intelligence agencies. The agencies were alleged in the documents to have signed on to a plan to discredit Islamic scholar and preacher Fethullah Gulen, who has lived in self-imposed exile in the United States since 1999.