A prosecutor in Istanbul charged Gen. Ilker Basbug, former chief of general staff, with leading a terrorist organization and attempting to overthrow the Turkish government, the Hurriyet Daily News reported.
The former army chief was taken to Istanbul's Silivri prison, the BBC reported.
Basbug, who retired in 2010, is the highest ranking military official arrested in an investigation of the Ergenekon network, a nationalist group that prosecutors allege tried to bring down Erdogan's government in 2003.
Basbug has denied the allegations.
The so-called Internet Memorandum case concerns allegations that the general staff distributed a document about setting up 42 Web sites to distribute propaganda against Erdogan's ruling Justice and Development Party, the banned Kurdistan Workers' Party, and Greeks and Armenians, the Hurriyet Daily News said.
Suspects have said several of the Web sites under investigation were set up with Basbug's knowledge and approval.
Media accounts indicate generals, admirals and colonels and journalists were among those arrested recently in the case.